pax_global_header00006660000000000000000000000064122071517710014515gustar00rootroot0000000000000052 comment=5e8b41d099a0deae7a179d5a75a5f302835a233c bioawk-1.0/000077500000000000000000000000001220715177100126315ustar00rootroot00000000000000bioawk-1.0/.gitigore000066400000000000000000000000131220715177100144350ustar00rootroot00000000000000*.o .*.swp bioawk-1.0/FIXES000066400000000000000000001050411220715177100134330ustar00rootroot00000000000000/**************************************************************** Copyright (C) Lucent Technologies 1997 All Rights Reserved Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that the copyright notice and this permission notice and warranty disclaimer appear in supporting documentation, and that the name Lucent Technologies or any of its entities not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ****************************************************************/ This file lists all bug fixes, changes, etc., made since the AWK book was sent to the printers in August, 1987. Aug 10, 2011: another fix to avoid core dump with delete(ARGV); again, many thanks to ruslan ermilov. Aug 7, 2011: split(s, a, //) now behaves the same as split(s, a, "") Jun 12, 2011: /pat/, \n /pat/ {...} is now legal, though bad style to use. added checks to new -v code that permits -vnospace; thanks to ruslan ermilov for spotting this and providing the patch. removed fixed limit on number of open files; thanks to aleksey cheusov and christos zoulos. fixed day 1 bug that resurrected deleted elements of ARGV when used as filenames (in lib.c). minor type fiddles to make gcc -Wall -pedantic happier (but not totally so); turned on -fno-strict-aliasing in makefile. May 6, 2011: added #ifdef for isblank. now allows -ffoo as well as -f foo arguments. (thanks, ruslan) May 1, 2011: after advice from todd miller, kevin lo, ruslan ermilov, and arnold robbins, changed srand() to return the previous seed (which is 1 on the first call of srand). the seed is an Awkfloat internally though converted to unsigned int to pass to the library srand(). thanks, everyone. fixed a subtle (and i hope low-probability) overflow error in fldbld, by adding space for one extra \0. thanks to robert bassett for spotting this one and providing a fix. removed the files related to compilation on windows. i no longer have anything like a current windows environment, so i can't test any of it. May 23, 2010: fixed long-standing overflow bug in run.c; many thanks to nelson beebe for spotting it and providing the fix. fixed bug that didn't parse -vd=1 properly; thanks to santiago vila for spotting it. Feb 8, 2010: i give up. replaced isblank with isspace in b.c; there are no consistent header files. Nov 26, 2009: fixed a long-standing issue with when FS takes effect. a change to FS is now noticed immediately for subsequent splits. changed the name getline() to awkgetline() to avoid yet another name conflict somewhere. Feb 11, 2009: temporarily for now defined HAS_ISBLANK, since that seems to be the best way through the thicket. isblank arrived in C99, but seems to be arriving at different systems at different times. Oct 8, 2008: fixed typo in b.c that set tmpvec wrongly. no one had ever run into the problem, apparently. thanks to alistair crooks. Oct 23, 2007: minor fix in lib.c: increase inputFS to 100, change malloc for fields to n+1. fixed memory fault caused by out of order test in setsval. thanks to david o'brien, freebsd, for both fixes. May 1, 2007: fiddle in makefile to fix for BSD make; thanks to igor sobrado. Mar 31, 2007: fixed some null pointer refs calling adjbuf. Feb 21, 2007: fixed a bug in matching the null RE in sub and gsub. thanks to al aho who actually did the fix (in b.c), and to wolfgang seeberg for finding it and providing a very compact test case. fixed quotation in b.c; thanks to Hal Pratt and the Princeton Dante Project. removed some no-effect asserts in run.c. fiddled maketab.c to not complain about bison-generated values. removed the obsolete -V argument; fixed --version to print the version and exit. fixed wording and an outright error in the usage message; thanks to igor sobrado and jason mcintyre. fixed a bug in -d that caused core dump if no program followed. Jan 1, 2007: dropped mac.code from makefile; there are few non-MacOSX mac's these days. Jan 17, 2006: system() not flagged as unsafe in the unadvertised -safe option. found it while enhancing tests before shipping the ;login: article. practice what you preach. removed the 9-years-obsolete -mr and -mf flags. added -version and --version options. core dump on linux with BEGIN {nextfile}, now fixed. removed some #ifdef's in run.c and lex.c that appear to no longer be necessary. Apr 24, 2005: modified lib.c so that values of $0 et al are preserved in the END block, apparently as required by posix. thanks to havard eidnes for the report and code. Jan 14, 2005: fixed infinite loop in parsing, originally found by brian tsang. thanks to arnold robbins for a suggestion that started me rethinking it. Dec 31, 2004: prevent overflow of -f array in main, head off potential error in call of SYNTAX(), test malloc return in lib.c, all with thanks to todd miller. Dec 22, 2004: cranked up size of NCHARS; coverity thinks it can be overrun with smaller size, and i think that's right. added some assertions to b.c to catch places where it might overrun. the RE code is still fragile. Dec 5, 2004: fixed a couple of overflow problems with ridiculous field numbers: e.g., print $(2^32-1). thanks to ruslan ermilov, giorgos keramidas and david o'brien at freebsd.org for patches. this really should be re-done from scratch. Nov 21, 2004: fixed another 25-year-old RE bug, in split. it's another failure to (re-)initialize. thanks to steve fisher for spotting this and providing a good test case. Nov 22, 2003: fixed a bug in regular expressions that dates (so help me) from 1977; it's been there from the beginning. an anchored longest match that was longer than the number of states triggered a failure to initialize the machine properly. many thanks to moinak ghosh for not only finding this one but for providing a fix, in some of the most mysterious code known to man. fixed a storage leak in call() that appears to have been there since 1983 or so -- a function without an explicit return that assigns a string to a parameter leaked a Cell. thanks to moinak ghosh for spotting this very subtle one. Jul 31, 2003: fixed, thanks to andrey chernov and ruslan ermilov, a bug in lex.c that mis-handled the character 255 in input. (it was being compared to EOF with a signed comparison.) Jul 29, 2003: fixed (i think) the long-standing botch that included the beginning of line state ^ for RE's in the set of valid characters; this led to a variety of odd problems, including failure to properly match certain regular expressions in non-US locales. thanks to ruslan for keeping at this one. Jul 28, 2003: n-th try at getting internationalization right, with thanks to volker kiefel, arnold robbins and ruslan ermilov for advice, though they should not be blamed for the outcome. according to posix, "." is the radix character in programs and command line arguments regardless of the locale; otherwise, the locale should prevail for input and output of numbers. so it's intended to work that way. i have rescinded the attempt to use strcoll in expanding shorthands in regular expressions (cclenter). its properties are much too surprising; for example [a-c] matches aAbBc in locale en_US but abBcC in locale fr_CA. i can see how this might arise by implementation but i cannot explain it to a human user. (this behavior can be seen in gawk as well; we're leaning on the same library.) the issue appears to be that strcoll is meant for sorting, where merging upper and lower case may make sense (though note that unix sort does not do this by default either). it is not appropriate for regular expressions, where the goal is to match specific patterns of characters. in any case, the notations [:lower:], etc., are available in awk, and they are more likely to work correctly in most locales. a moratorium is hereby declared on internationalization changes. i apologize to friends and colleagues in other parts of the world. i would truly like to get this "right", but i don't know what that is, and i do not want to keep making changes until it's clear. Jul 4, 2003: fixed bug that permitted non-terminated RE, as in "awk /x". Jun 1, 2003: subtle change to split: if source is empty, number of elems is always 0 and the array is not set. Mar 21, 2003: added some parens to isblank, in another attempt to make things internationally portable. Mar 14, 2003: the internationalization changes, somewhat modified, are now reinstated. in theory awk will now do character comparisons and case conversions in national language, but "." will always be the decimal point separator on input and output regardless of national language. isblank(){} has an #ifndef. this no longer compiles on windows: LC_MESSAGES isn't defined in vc6++. fixed subtle behavior in field and record splitting: if FS is a single character and RS is not empty, \n is NOT a separator. this tortuous reading is found in the awk book; behavior now matches gawk and mawk. Dec 13, 2002: for the moment, the internationalization changes of nov 29 are rolled back -- programs like x = 1.2 don't work in some locales, because the parser is expecting x = 1,2. until i understand this better, this will have to wait. Nov 29, 2002: modified b.c (with tiny changes in main and run) to support locales, using strcoll and iswhatever tests for posix character classes. thanks to ruslan ermilov (ru@freebsd.org) for code. the function isblank doesn't seem to have propagated to any header file near me, so it's there explicitly. not properly tested on non-ascii character sets by me. Jun 28, 2002: modified run/format() and tran/getsval() to do a slightly better job on using OFMT for output from print and CONVFMT for other number->string conversions, as promised by posix and done by gawk and mawk. there are still places where it doesn't work right if CONVFMT is changed; by then the STR attribute of the variable has been irrevocably set. thanks to arnold robbins for code and examples. fixed subtle bug in format that could get core dump. thanks to Jaromir Dolecek for finding and fixing. minor cleanup in run.c / format() at the same time. added some tests for null pointers to debugging printf's, which were never intended for external consumption. thanks to dave kerns (dkerns@lucent.com) for pointing this out. GNU compatibility: an empty regexp matches anything (thanks to dag-erling smorgrav, des@ofug.org). subject to reversion if this does more harm than good. pervasive small changes to make things more const-correct, as reported by gcc's -Wwrite-strings. as it says in the gcc manual, this may be more nuisance than useful. provoked by a suggestion and code from arnaud desitter, arnaud@nimbus.geog.ox.ac.uk minor documentation changes to note that this now compiles out of the box on Mac OS X. Feb 10, 2002: changed types in posix chars structure to quiet solaris cc. Jan 1, 2002: fflush() or fflush("") flushes all files and pipes. length(arrayname) returns number of elements; thanks to arnold robbins for suggestion. added a makefile.win to make it easier to build on windows. based on dan allen's buildwin.bat. Nov 16, 2001: added support for posix character class names like [:digit:], which are not exactly shorter than [0-9] and perhaps no more portable. thanks to dag-erling smorgrav for code. Feb 16, 2001: removed -m option; no longer needed, and it was actually broken (noted thanks to volker kiefel). Feb 10, 2001: fixed an appalling bug in gettok: any sequence of digits, +,-, E, e, and period was accepted as a valid number if it started with a period. this would never have happened with the lex version. other 1-character botches, now fixed, include a bare $ and a bare " at the end of the input. Feb 7, 2001: more (const char *) casts in b.c and tran.c to silence warnings. Nov 15, 2000: fixed a bug introduced in august 1997 that caused expressions like $f[1] to be syntax errors. thanks to arnold robbins for noticing this and providing a fix. Oct 30, 2000: fixed some nextfile bugs: not handling all cases. thanks to arnold robbins for pointing this out. new regressions added. close() is now a function. it returns whatever the library fclose returns, and -1 for closing a file or pipe that wasn't opened. Sep 24, 2000: permit \n explicitly in character classes; won't work right if comes in as "[\n]" but ok as /[\n]/, because of multiple processing of \'s. thanks to arnold robbins. July 5, 2000: minor fiddles in tran.c to keep compilers happy about uschar. thanks to norman wilson. May 25, 2000: yet another attempt at making 8-bit input work, with another band-aid in b.c (member()), and some (uschar) casts to head off potential errors in subscripts (like isdigit). also changed HAT to NCHARS-2. thanks again to santiago vila. changed maketab.c to ignore apparently out of range definitions instead of halting; new freeBSD generates one. thanks to jon snader for pointing out the problem. May 2, 2000: fixed an 8-bit problem in b.c by making several char*'s into unsigned char*'s. not clear i have them all yet. thanks to Santiago Vila for the bug report. Apr 21, 2000: finally found and fixed a memory leak in function call; it's been there since functions were added ~1983. thanks to jon bentley for the test case that found it. added test in envinit to catch environment "variables" with names beginning with '='; thanks to Berend Hasselman. Jul 28, 1999: added test in defn() to catch function foo(foo), which otherwise recurses until core dump. thanks to arnold robbins for noticing this. Jun 20, 1999: added *bp in gettok in lex.c; appears possible to exit function without terminating the string. thanks to russ cox. Jun 2, 1999: added function stdinit() to run to initialize files[] array, in case stdin, etc., are not constants; some compilers care. May 10, 1999: replaced the ERROR ... FATAL, etc., macros with functions based on vprintf, to avoid problems caused by overrunning fixed-size errbuf array. thanks to ralph corderoy for the impetus, and for pointing out a string termination bug in qstring as well. Apr 21, 1999: fixed bug that caused occasional core dumps with commandline variable with value ending in \. (thanks to nelson beebe for the test case.) Apr 16, 1999: with code kindly provided by Bruce Lilly, awk now parses /=/ and similar constructs more sensibly in more places. Bruce also provided some helpful test cases. Apr 5, 1999: changed true/false to True/False in run.c to make it easier to compile with C++. Added some casts on malloc and realloc to be honest about casts; ditto. changed ltype int to long in struct rrow to reduce some 64-bit complaints; other changes scattered throughout for the same purpose. thanks to Nelson Beebe for these portability improvements. removed some horrible pointer-int casting in b.c and elsewhere by adding ptoi and itonp to localize the casts, which are all benign. fixed one incipient bug that showed up on sgi in 64-bit mode. reset lineno for new source file; include filename in error message. also fixed line number error in continuation lines. (thanks to Nelson Beebe for both of these.) Mar 24, 1999: Nelson Beebe notes that irix 5.3 yacc dies with a bogus error; use a newer version or switch to bison, since sgi is unlikely to fix it. Mar 5, 1999: changed isnumber to is_number to avoid the problem caused by versions of ctype.h that include the name isnumber. distribution now includes a script for building on a Mac, thanks to Dan Allen. Feb 20, 1999: fixed memory leaks in run.c (call) and tran.c (setfval). thanks to Stephen Nutt for finding these and providing the fixes. Jan 13, 1999: replaced srand argument by (unsigned int) in run.c; avoids problem on Mac and potentially on Unix & Windows. thanks to Dan Allen. added a few (int) casts to silence useless compiler warnings. e.g., errorflag= in run.c jump(). added proctab.c to the bundle outout; one less thing to have to compile out of the box. added calls to _popen and _pclose to the win95 stub for pipes (thanks to Steve Adams for this helpful suggestion). seems to work, though properties are not well understood by me, and it appears that under some circumstances the pipe output is truncated. Be careful. Oct 19, 1998: fixed a couple of bugs in getrec: could fail to update $0 after a getline var; because inputFS wasn't initialized, could split $0 on every character, a misleading diversion. fixed caching bug in makedfa: LRU was actually removing least often used. thanks to ross ridge for finding these, and for providing great bug reports. May 12, 1998: fixed potential bug in readrec: might fail to update record pointer after growing. thanks to dan levy for spotting this and suggesting the fix. Mar 12, 1998: added -V to print version number and die. Feb 11, 1998: subtle silent bug in lex.c: if the program ended with a number longer than 1 digit, part of the input would be pushed back and parsed again because token buffer wasn't terminated right. example: awk 'length($0) > 10'. blush. at least i found it myself. Aug 31, 1997: s/adelete/awkdelete/: SGI uses this in malloc.h. thanks to nelson beebe for pointing this one out. Aug 21, 1997: fixed some bugs in sub and gsub when replacement includes \\. this is a dark, horrible corner, but at least now i believe that the behavior is the same as gawk and the intended posix standard. thanks to arnold robbins for advice here. Aug 9, 1997: somewhat regretfully, replaced the ancient lex-based lexical analyzer with one written in C. it's longer, generates less code, and more portable; the old one depended too much on mysterious properties of lex that were not preserved in other environments. in theory these recognize the same language. now using strtod to test whether a string is a number, instead of the convoluted original function. should be more portable and reliable if strtod is implemented right. removed now-pointless optimization in makefile that tries to avoid recompilation when awkgram.y is changed but symbols are not. removed most fixed-size arrays, though a handful remain, some of which are unchecked. you have been warned. Aug 4, 1997: with some trepidation, replaced the ancient code that managed fields and $0 in fixed-size arrays with arrays that grow on demand. there is still some tension between trying to make this run fast and making it clean; not sure it's right yet. the ill-conceived -mr and -mf arguments are now useful only for debugging. previous dynamic string code removed. numerous other minor cleanups along the way. Jul 30, 1997: using code provided by dan levy (to whom profuse thanks), replaced fixed-size arrays and awkward kludges by a fairly uniform mechanism to grow arrays as needed for printf, sub, gsub, etc. Jul 23, 1997: falling off the end of a function returns "" and 0, not 0. thanks to arnold robbins. Jun 17, 1997: replaced several fixed-size arrays by dynamically-created ones in run.c; added overflow tests to some previously unchecked cases. getline, toupper, tolower. getline code is still broken in that recursive calls may wind up using the same space. [fixed later] increased RECSIZE to 8192 to push problems further over the horizon. added \r to \n as input line separator for programs, not data. damn CRLFs. modified format() to permit explicit printf("%c", 0) to include a null byte in output. thanks to ken stailey for the fix. added a "-safe" argument that disables file output (print >, print >>), process creation (cmd|getline, print |, system), and access to the environment (ENVIRON). this is a first approximation to a "safe" version of awk, but don't rely on it too much. thanks to joan feigenbaum and matt blaze for the inspiration long ago. Jul 8, 1996: fixed long-standing bug in sub, gsub(/a/, "\\\\&"); thanks to ralph corderoy. Jun 29, 1996: fixed awful bug in new field splitting; didn't get all the places where input was done. Jun 28, 1996: changed field-splitting to conform to posix definition: fields are split using the value of FS at the time of input; it used to be the value when the field or NF was first referred to, a much less predictable definition. thanks to arnold robbins for encouragement to do the right thing. May 28, 1996: fixed appalling but apparently unimportant bug in parsing octal numbers in reg exprs. explicit hex in reg exprs now limited to 2 chars: \xa, \xaa. May 27, 1996: cleaned up some declarations so gcc -Wall is now almost silent. makefile now includes backup copies of ytab.c and lexyy.c in case one makes before looking; it also avoids recreating lexyy.c unless really needed. s/aprintf/awkprint, s/asprintf/awksprintf/ to avoid some name clashes with unwisely-written header files. thanks to jeffrey friedl for several of these. May 26, 1996: an attempt to rationalize the (unsigned) char issue. almost all instances of unsigned char have been removed; the handful of places in b.c where chars are used as table indices have been hand-crafted. added some latin-1 tests to the regression, but i'm not confident; none of my compilers seem to care much. thanks to nelson beebe for pointing out some others that do care. May 2, 1996: removed all register declarations. enhanced split(), as in gawk, etc: split(s, a, "") splits s into a[1]...a[length(s)] with each character a single element. made the same changes for field-splitting if FS is "". added nextfile, as in gawk: causes immediate advance to next input file. (thanks to arnold robbins for inspiration and code). small fixes to regexpr code: can now handle []], [[], and variants; [] is now a syntax error, rather than matching everything; [z-a] is now empty, not z. far from complete or correct, however. (thanks to jeffrey friedl for pointing out some awful behaviors.) Apr 29, 1996: replaced uchar by uschar everywhere; apparently some compilers usurp this name and this causes conflicts. fixed call to time in run.c (bltin); arg is time_t *. replaced horrible pointer/long punning in b.c by a legitimate union. should be safer on 64-bit machines and cleaner everywhere. (thanks to nelson beebe for pointing out some of these problems.) replaced nested comments by #if 0...#endif in run.c, lib.c. removed getsval, setsval, execute macros from run.c and lib.c. machines are 100x faster than they were when these macros were first used. revised filenames: awk.g.y => awkgram.y, awk.lx.l => awklex.l, y.tab.[ch] => ytab.[ch], lex.yy.c => lexyy.c, all in the aid of portability to nameless systems. "make bundle" now includes yacc and lex output files for recipients who don't have yacc or lex. Aug 15, 1995: initialized Cells in setsymtab more carefully; some fields were not set. (thanks to purify, all of whose complaints i think i now understand.) fixed at least one error in gsub that looked at -1-th element of an array when substituting for a null match (e.g., $). delete arrayname is now legal; it clears the elements but leaves the array, which may not be the right behavior. modified makefile: my current make can't cope with the test used to avoid unnecessary yacc invocations. Jul 17, 1995: added dynamically growing strings to awk.lx.l and b.c to permit regular expressions to be much bigger. the state arrays can still overflow. Aug 24, 1994: detect duplicate arguments in function definitions (mdm). May 11, 1994: trivial fix to printf to limit string size in sub(). Apr 22, 1994: fixed yet another subtle self-assignment problem: $1 = $2; $1 = $1 clobbered $1. Regression tests now use private echo, to avoid quoting problems. Feb 2, 1994: changed error() to print line number as %d, not %g. Jul 23, 1993: cosmetic changes: increased sizes of some arrays, reworded some error messages. added CONVFMT as in posix (just replaced OFMT in getsval) FILENAME is now "" until the first thing that causes a file to be opened. Nov 28, 1992: deleted yyunput and yyoutput from proto.h; different versions of lex give these different declarations. May 31, 1992: added -mr N and -mf N options: more record and fields. these really ought to adjust automatically. cleaned up some error messages; "out of space" now means malloc returned NULL in all cases. changed rehash so that if it runs out, it just returns; things will continue to run slow, but maybe a bit longer. Apr 24, 1992: remove redundant close of stdin when using -f -. got rid of core dump with -d; awk -d just prints date. Apr 12, 1992: added explicit check for /dev/std(in,out,err) in redirection. unlike gawk, no /dev/fd/n yet. added (file/pipe) builtin. hard to test satisfactorily. not posix. Feb 20, 1992: recompile after abortive changes; should be unchanged. Dec 2, 1991: die-casting time: converted to ansi C, installed that. Nov 30, 1991: fixed storage leak in freefa, failing to recover [N]CCL. thanks to Bill Jones (jones@cs.usask.ca) Nov 19, 1991: use RAND_MAX instead of literal in builtin(). Nov 12, 1991: cranked up some fixed-size arrays in b.c, and added a test for overflow in penter. thanks to mark larsen. Sep 24, 1991: increased buffer in gsub. a very crude fix to a general problem. and again on Sep 26. Aug 18, 1991: enforce variable name syntax for commandline variables: has to start with letter or _. Jul 27, 1991: allow newline after ; in for statements. Jul 21, 1991: fixed so that in self-assignment like $1=$1, side effects like recomputing $0 take place. (this is getting subtle.) Jun 30, 1991: better test for detecting too-long output record. Jun 2, 1991: better defense against very long printf strings. made break and continue illegal outside of loops. May 13, 1991: removed extra arg on gettemp, tempfree. minor error message rewording. May 6, 1991: fixed silly bug in hex parsing in hexstr(). removed an apparently unnecessary test in isnumber(). warn about weird printf conversions. fixed unchecked array overwrite in relex(). changed for (i in array) to access elements in sorted order. then unchanged it -- it really does run slower in too many cases. left the code in place, commented out. Feb 10, 1991: check error status on all writes, to avoid banging on full disks. Jan 28, 1991: awk -f - reads the program from stdin. Jan 11, 1991: failed to set numeric state on $0 in cmd|getline context in run.c. Nov 2, 1990: fixed sleazy test for integrality in getsval; use modf. Oct 29, 1990: fixed sleazy buggy code in lib.c that looked (incorrectly) for too long input lines. Oct 14, 1990: fixed the bug on p. 198 in which it couldn't deduce that an argument was an array in some contexts. replaced the error message in intest() by code that damn well makes it an array. Oct 8, 1990: fixed horrible bug: types and values were not preserved in some kinds of self-assignment. (in assign().) Aug 24, 1990: changed NCHARS to 256 to handle 8-bit characters in strings presented to match(), etc. Jun 26, 1990: changed struct rrow (awk.h) to use long instead of int for lval, since cfoll() stores a pointer in it. now works better when int's are smaller than pointers! May 6, 1990: AVA fixed the grammar so that ! is uniformly of the same precedence as unary + and -. This renders illegal some constructs like !x=y, which now has to be parenthesized as !(x=y), and makes others work properly: !x+y is (!x)+y, and x!y is x !y, not two pattern-action statements. (These problems were pointed out by Bob Lenk of Posix.) Added \x to regular expressions (already in strings). Limited octal to octal digits; \8 and \9 are not octal. Centralized the code for parsing escapes in regular expressions. Added a bunch of tests to T.re and T.sub to verify some of this. Feb 9, 1990: fixed null pointer dereference bug in main.c: -F[nothing]. sigh. restored srand behavior: it returns the current seed. Jan 18, 1990: srand now returns previous seed value (0 to start). Jan 5, 1990: fix potential problem in tran.c -- something was freed, then used in freesymtab. Oct 18, 1989: another try to get the max number of open files set with relatively machine-independent code. small fix to input() in case of multiple reads after EOF. Oct 11, 1989: FILENAME is now defined in the BEGIN block -- too many old programs broke. "-" means stdin in getline as well as on the commandline. added a bunch of casts to the code to tell the truth about char * vs. unsigned char *, a right royal pain. added a setlocale call to the front of main, though probably no one has it usefully implemented yet. Aug 24, 1989: removed redundant relational tests against nullnode if parse tree already had a relational at that point. Aug 11, 1989: fixed bug: commandline variable assignment has to look like var=something. (consider the man page for =, in file =.1) changed number of arguments to functions to static arrays to avoid repeated malloc calls. Aug 2, 1989: restored -F (space) separator Jul 30, 1989: added -v x=1 y=2 ... for immediate commandline variable assignment; done before the BEGIN block for sure. they have to precede the program if the program is on the commandline. Modified Aug 2 to require a separate -v for each assignment. Jul 10, 1989: fixed ref-thru-zero bug in environment code in tran.c Jun 23, 1989: add newline to usage message. Jun 14, 1989: added some missing ansi printf conversion letters: %i %X %E %G. no sensible meaning for h or L, so they may not do what one expects. made %* conversions work. changed x^y so that if n is a positive integer, it's done by explicit multiplication, thus achieving maximum accuracy. (this should be done by pow() but it seems not to be locally.) done to x ^= y as well. Jun 4, 1989: ENVIRON array contains environment: if shell variable V=thing, ENVIRON["V"] is "thing" multiple -f arguments permitted. error reporting is naive. (they were permitted before, but only the last was used.) fixed a really stupid botch in the debugging macro dprintf fixed order of evaluation of commandline assignments to match what the book claims: an argument of the form x=e is evaluated at the time it would have been opened if it were a filename (p 63). this invalidates the suggested answer to ex 4-1 (p 195). removed some code that permitted -F (space) fieldseparator, since it didn't quite work right anyway. (restored aug 2) Apr 27, 1989: Line number now accumulated correctly for comment lines. Apr 26, 1989: Debugging output now includes a version date, if one compiles it into the source each time. Apr 9, 1989: Changed grammar to prohibit constants as 3rd arg of sub and gsub; prevents class of overwriting-a-constant errors. (Last one?) This invalidates the "banana" example on page 43 of the book. Added \a ("alert"), \v (vertical tab), \xhhh (hexadecimal), as in ANSI, for strings. Rescinded the sloppiness that permitted non-octal digits in \ooo. Warning: not all compilers and libraries will be able to deal with \x correctly. Jan 9, 1989: Fixed bug that caused tempcell list to contain a duplicate. The fix is kludgy. Dec 17, 1988: Catches some more commandline errors in main. Removed redundant decl of modf in run.c (confuses some compilers). Warning: there's no single declaration of malloc, etc., in awk.h that seems to satisfy all compilers. Dec 7, 1988: Added a bit of code to error printing to avoid printing nulls. (Not clear that it actually would.) Nov 27, 1988: With fear and trembling, modified the grammar to permit multiple pattern-action statements on one line without an explicit separator. By definition, this capitulation to the ghost of ancient implementations remains undefined and thus subject to change without notice or apology. DO NOT COUNT ON IT. Oct 30, 1988: Fixed bug in call() that failed to recover storage. A warning is now generated if there are more arguments in the call than in the definition (in lieu of fixing another storage leak). Oct 20, 1988: Fixed %c: if expr is numeric, use numeric value; otherwise print 1st char of string value. still doesn't work if the value is 0 -- won't print \0. Added a few more checks for running out of malloc. Oct 12, 1988: Fixed bug in call() that freed local arrays twice. Fixed to handle deletion of non-existent array right; complains about attempt to delete non-array element. Sep 30, 1988: Now guarantees to evaluate all arguments of built-in functions, as in C; the appearance is that arguments are evaluated before the function is called. Places affected are sub (gsub was ok), substr, printf, and all the built-in arithmetic functions in bltin(). A warning is generated if a bltin() is called with the wrong number of arguments. This requires changing makeprof on p167 of the book. Aug 23, 1988: setting FILENAME in BEGIN caused core dump, apparently because it was freeing space not allocated by malloc. July 24, 1988: fixed egregious error in toupper/tolower functions. still subject to rescinding, however. July 2, 1988: flush stdout before opening file or pipe July 2, 1988: performance bug in b.c/cgoto(): not freeing some sets of states. partial fix only right now, and the number of states increased to make it less obvious. June 1, 1988: check error status on close May 28, 1988: srand returns seed value it's using. see 1/18/90 May 22, 1988: Removed limit on depth of function calls. May 10, 1988: Fixed lib.c to permit _ in commandline variable names. Mar 25, 1988: main.c fixed to recognize -- as terminator of command- line options. Illegal options flagged. Error reporting slightly cleaned up. Dec 2, 1987: Newer C compilers apply a strict scope rule to extern declarations within functions. Two extern declarations in lib.c and tran.c have been moved to obviate this problem. Oct xx, 1987: Reluctantly added toupper and tolower functions. Subject to rescinding without notice. Sep 17, 1987: Error-message printer had printf(s) instead of printf("%s",s); got core dumps when the message included a %. Sep 12, 1987: Very long printf strings caused core dump; fixed aprintf, asprintf, format to catch them. Can still get a core dump in printf itself. bioawk-1.0/Makefile000066400000000000000000000041341220715177100142730ustar00rootroot00000000000000# /**************************************************************** # Copyright (C) Lucent Technologies 1997 # All Rights Reserved # # Permission to use, copy, modify, and distribute this software and # its documentation for any purpose and without fee is hereby # granted, provided that the above copyright notice appear in all # copies and that both that the copyright notice and this # permission notice and warranty disclaimer appear in supporting # documentation, and that the name Lucent Technologies or any of # its entities not be used in advertising or publicity pertaining # to distribution of the software without specific, written prior # permission. # # LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, # INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. # IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY # SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER # IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, # ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF # THIS SOFTWARE. # ****************************************************************/ CFLAGS = -g -Wall -O2 CC = gcc YACC = bison -y YACC = yacc YFLAGS = -d OFILES = b.o main.o parse.o proctab.o tran.o lib.o run.o lex.o addon.o SOURCE = awk.h ytab.c ytab.h proto.h awkgram.y lex.c b.c main.c \ maketab.c parse.c lib.c run.c tran.c proctab.c addon.c LISTING = awk.h proto.h awkgram.y lex.c b.c main.c maketab.c parse.c \ lib.c run.c tran.c addon.c SHIP = README FIXES $(SOURCE) ytab[ch].bak makefile \ awk.1 bioawk:ytab.o $(OFILES) $(CC) $(CFLAGS) ytab.o $(OFILES) $(ALLOC) -o $@ -lm -lz $(OFILES): awk.h ytab.h proto.h addon.h ytab.o: awk.h proto.h awkgram.y $(YACC) $(YFLAGS) awkgram.y mv y.tab.c ytab.c mv y.tab.h ytab.h $(CC) $(CFLAGS) -c ytab.c proctab.c: maketab ./maketab >proctab.c maketab: ytab.h maketab.c $(CC) $(CFLAGS) maketab.c -o maketab names: @echo $(LISTING) clean: rm -fr a.out *.o *.obj maketab maketab.exe *.bb *.bbg *.da *.gcov *.gcno *.gcda awk ytab.* proctab.c *.dSYM bioawk-1.0/README.awk000066400000000000000000000074201220715177100142750ustar00rootroot00000000000000/**************************************************************** Copyright (C) Lucent Technologies 1997 All Rights Reserved Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that the copyright notice and this permission notice and warranty disclaimer appear in supporting documentation, and that the name Lucent Technologies or any of its entities not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ****************************************************************/ This is the version of awk described in "The AWK Programming Language", by Al Aho, Brian Kernighan, and Peter Weinberger (Addison-Wesley, 1988, ISBN 0-201-07981-X). Changes, mostly bug fixes and occasional enhancements, are listed in FIXES. If you distribute this code further, please please please distribute FIXES with it. If you find errors, please report them to bwk@cs.princeton.edu. Thanks. The program itself is created by make which should produce a sequence of messages roughly like this: yacc -d awkgram.y conflicts: 43 shift/reduce, 85 reduce/reduce mv y.tab.c ytab.c mv y.tab.h ytab.h cc -c ytab.c cc -c b.c cc -c main.c cc -c parse.c cc maketab.c -o maketab ./maketab >proctab.c cc -c proctab.c cc -c tran.c cc -c lib.c cc -c run.c cc -c lex.c cc ytab.o b.o main.o parse.o proctab.o tran.o lib.o run.o lex.o -lm This produces an executable a.out; you will eventually want to move this to some place like /usr/bin/awk. If your system does not have yacc or bison (the GNU equivalent), you must compile the pieces manually. We have included yacc output in ytab.c and ytab.h, and backup copies in case you overwrite them. We have also included a copy of proctab.c so you do not need to run maketab. NOTE: This version uses ANSI C, as you should also. We have compiled this without any changes using gcc -Wall and/or local C compilers on a variety of systems, but new systems or compilers may raise some new complaint; reports of difficulties are welcome. This also compiles with Visual C++ on all flavors of Windows, *if* you provide versions of popen and pclose. The file missing95.c contains versions that can be used to get started with, though the underlying support has mysterious properties, the symptom of which can be truncated pipe output. Beware. The file makefile.win gives hints on how to proceed; if you run vcvars32.bat, it will set up necessary paths and parameters so you can subsequently run nmake -f makefile.win. Beware also that when running on Windows under command.com, various quoting conventions are different from Unix systems: single quotes won't work around arguments, and various characters like % are interpreted within double quotes. This compiles without change on Macintosh OS X using gcc and the standard developer tools. This is also said to compile on Macintosh OS 9 systems, using the file "buildmac" provided by Dan Allen (danallen@microsoft.com), to whom many thanks. The version of malloc that comes with some systems is sometimes astonishly slow. If awk seems slow, you might try fixing that. More generally, turning on optimization can significantly improve awk's speed, perhaps by 1/3 for highest levels. bioawk-1.0/README.md000066400000000000000000000056751220715177100141250ustar00rootroot00000000000000###Introduction Bioawk is an extension to [Brian Kernighan's awk][1], adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and an command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk. ###New functionality #####Command line option `-t` Using this option is equivalent to bioawk -F'\t' -v OFS="\t" #####Command line option `-c arg` This option specifies the input format. When this option is in use, bioawk will seamlessly add variables that name the fields, based on either the format or the first line of the input, depending *arg*. This option also enables bioawk to read gzip'd files. The argument *arg* may take the following values: * `help`. List the supported formats and the naming variables. * `hdr` or `header`. Name each column based on the first line in the input. Special characters in the first are converted to underscore. For example: grep -v ^## in.vcf | bioawk -tc hdr '{print $_CHROM,$POS}' prints the `CHROM` and `POS` columns of the input VCF file. * `sam`, `vcf`, `bed` and `gff`. SAM, VCF, BED and GFF formats. * `fastx`. This option regards a FASTA or FASTQ as a TAB delimited file with four columns: sequence name, sequence, quality and FASTA/Q comment, such that various fields can be retrieved with column names. See also example 4 in the following. #####New built-in functions See `awk.1`. ###Examples 1. List the supported formats: bioawk -c help 2. Extract unmapped reads without header: bioawk -c sam 'and($flag,4)' aln.sam.gz 3. Extract mapped reads with header: bioawk -Hc sam '!and($flag,4)' 4. Reverse complement FASTA: bioawk -c fastx '{print ">"$name;print revcomp($seq)}' seq.fa.gz 5. Create FASTA from SAM (uses revcomp if FLAG & 16) samtools view aln.bam | \ bioawk -c sam '{s=$seq; if(and($flag, 16)) {s=revcomp($seq)} print ">"$qname"\n"s}' 6. Print the genotypes of sample `foo` and `bar` from a VCF: grep -v ^## in.vcf | bioawk -tc hdr '{print $foo,$bar}' ###Potential limitations 1. When option `-c` is in use, bioawk replaces the line reading module of awk. The new line reading function parses FASTA and FASTQ files and seamlessly reads gzip'ed files. However, the new code does not fully mimic the original code. It may fail in corner cases (though this has not happened yet). Thus when `-c` is not specified, awk falls back to the original line reading code and does not support gzip'ed input. 2. When `-c` is in use, several strings allocated in the new line reading module are not freed in the end. These will be reported by valgrind as "still reachable". To some extent, these are not memory leaks. [1]: http://www.cs.princeton.edu/~bwk/btl.mirror/ bioawk-1.0/addon.c000066400000000000000000000244201220715177100140640ustar00rootroot00000000000000#include #include #include #include #include #include "awk.h" int bio_flag = 0, bio_fmt = BIO_NULL; static const char *col_defs[][15] = { /* FIXME: this is convenient, but not memory efficient. Shouldn't matter. */ {"header", NULL}, {"bed", "chrom", "start", "end", "name", "score", "strand", "thickstart", "thickend", "rgb", "blockcount", "blocksizes", "blockstarts", NULL}, {"sam", "qname", "flag", "rname", "pos", "mapq", "cigar", "rnext", "pnext", "tlen", "seq", "qual", NULL}, {"vcf", "chrom", "pos", "id", "ref", "alt", "qual", "filter", "info", NULL}, {"gff", "seqname", "source", "feature", "start", "end", "score", "filter", "strand", "group", "attribute", NULL}, {"fastx", "name", "seq", "qual", "comment", NULL}, {NULL} }; static const char *tab_delim = "nyyyyyn", *hdr_chr = "\0#@##\0\0"; /************************ * Setting column names * ************************/ static void set_colnm_aux(const char *p, int col) { const char *q; char *r = 0; Cell *x; for (q = p; *q; ++q) /* test if there are punctuations */ if (ispunct(*q) && *q != '_') break; if (*q || isdigit(*p)) { /* there are punctuations or the first is digit */ char *qq; r = malloc(strlen(p) + 2); if (isdigit(*p)) { *r = '_'; strcpy(r + 1, p); } else strcpy(r, p); for (qq = r; *qq; ++qq) if (ispunct(*qq)) *qq = '_'; q = r; } else q = p; if ((x = lookup(q, symtab)) != NULL) /* do not add if not appear in the program */ setfval(x, (Awkfloat)col); if (r) free(r); } int bio_get_fmt(const char *s) { int i, j; if (strcmp(s, "hdr") == 0) return BIO_HDR; for (i = 0; col_defs[i][0]; ++i) if (strcmp(s, col_defs[i][0]) == 0) return i; for (i = 1; col_defs[i][0]; ++i) { printf("%s:\n\t", col_defs[i][0]); for (j = 1; col_defs[i][j]; ++j) printf("%d:%s ", j, col_defs[i][j]); putchar('\n'); } return BIO_NULL; } int bio_skip_hdr(const char *r) { if (bio_fmt <= BIO_HDR) return 0; if (*r && *r == hdr_chr[bio_fmt]) { if (bio_flag & BIO_SHOW_HDR) puts(r); return 1; } else return 0; } void bio_set_colnm() { int i; if (bio_fmt == BIO_NULL) { return; } else if (bio_fmt == BIO_HDR) { char *p, *q, c; for (p = record; *p && isspace(*p); ++p); /* skip leading spaces */ for (i = 1, q = p; *q; ++q) { if (!isspace(*q)) continue; c = *q; /* backup the space */ *q = 0; /* terminate the field */ set_colnm_aux(p, i); *q = c; /* change back */ ++i; for (p = q + 1; *p && isspace(*p); ++p); /* skip contiguous spaces */ q = p; } set_colnm_aux(p, i); /* the last column */ } else { for (i = 0; col_defs[bio_fmt][i] != NULL; ++i) set_colnm_aux(col_defs[bio_fmt][i], i); if (tab_delim[bio_fmt] == 'y') *FS = *OFS = "\t"; } } /********************** * Built-in functions * **********************/ static char comp_tab[] = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O', 'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z', 91, 92, 93, 94, 95, 64, 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o', 'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127 }; static float q_int2real[128]; #define tempfree(x) if (istemp(x)) tfree(x); else Cell *bio_func(int f, Cell *x, Node **a) { Cell *y, *z; y = gettemp(); if (f == BIO_FAND) { if (a[1]->nnext == 0) { WARNING("and requires two arguments; returning 0.0"); setfval(y, 0.0); } else { z = execute(a[1]->nnext); setfval(y, (Awkfloat)((long)getfval(x) & (long)getfval(z))); /* FIXME: does (long) always work??? */ tempfree(z); } } else if (f == BIO_FOR) { if (a[1]->nnext == 0) { WARNING("or requires two arguments; returning 0.0"); setfval(y, 0.0); } else { z = execute(a[1]->nnext); setfval(y, (Awkfloat)((long)getfval(x) | (long)getfval(z))); tempfree(z); } } else if (f == BIO_FXOR) { if (a[1]->nnext == 0) { WARNING("xor requires two arguments; returning 0.0"); setfval(y, 0.0); } else { z = execute(a[1]->nnext); setfval(y, (Awkfloat)((long)getfval(x) ^ (long)getfval(z))); tempfree(z); } } else if (f == BIO_FREVERSE) { char *buf = getsval(x); int i, l, tmp; l = strlen(buf); for (i = 0; i < l>>1; ++i) tmp = buf[i], buf[i] = buf[l-1-i], buf[l-1-i] = tmp; setsval(y, buf); } else if (f == BIO_FREVCOMP) { char *buf; int i, l, tmp; buf = getsval(x); l = strlen(buf); for (i = 0; i < l>>1; ++i) tmp = comp_tab[(int)buf[i]], buf[i] = comp_tab[(int)buf[l-1-i]], buf[l-1-i] = tmp; if (l&1) buf[l>>1] = comp_tab[(int)buf[l>>1]]; setsval(y, buf); } else if (f == BIO_FGC) { char *buf; int i, l, gc = 0; buf = getsval(x); l = strlen(buf); if (l) { /* don't try for empty strings */ for (i = 0; i < l; ++i) if (buf[i] == 'g' || buf[i] == 'c' || buf[i] == 'G' || buf[i] == 'C') gc++; setfval(y, (Awkfloat)gc / l); } } else if (f == BIO_FMEANQUAL) { char *buf; int i, l, total_qual = 0; buf = getsval(x); l = strlen(buf); if (l) { /* don't try for empty strings */ for (i = 0; i < l; ++i) total_qual += buf[i] - 33; setfval(y, (Awkfloat)total_qual / l); } } else if (f == BIO_FTRIMQ) { char *buf; double thres = 0.05, s, max; int i, l, tmp, beg, end; Cell *u = 0, *v = 0; if (a[1]->nnext) { u = execute(a[1]->nnext); /* begin */ if (a[1]->nnext->nnext) { v = execute(a[1]->nnext->nnext); /* end */ if (a[1]->nnext->nnext->nnext) { z = execute(a[1]->nnext->nnext->nnext); thres = getfval(z); /* user defined threshold */ tempfree(z); } } } buf = getsval(x); l = strlen(buf); if (q_int2real[0] == 0.) /* to initialize */ for (i = 0; i < 128; ++i) q_int2real[i] = pow(10., -(i - 33) / 10.); for (i = 0, beg = tmp = 0, end = l, s = max = 0.; i < l; ++i) { int q = buf[i]; if (q < 36) q = 36; if (q > 127) q = 127; s += thres - q_int2real[q]; if (s > max) max = s, beg = tmp, end = i + 1; if (s < 0) s = 0, tmp = i + 1; } if (u) { setfval(u, beg); tempfree(u); } /* 1-based position; as substr() is 1-based. */ if (v) { setfval(v, end); tempfree(v); } } else if (f == BIO_FQUALCOUNT) { if (a[1]->nnext == 0) { WARNING("qualcount requires two arguments; returning 0.0"); setfval(y, 0.0); } else { char *buf; int i, l, thres, cnt = 0; buf = getsval(x); l = strlen(buf); z = execute(a[1]->nnext); /* threshold */ thres = (int)(getfval(z) + .499); for (i = 0; i < l; ++i) if (buf[i] - 33 >= thres) ++cnt; setfval(y, (Awkfloat)cnt); } } /* else: never happens */ return y; } /************************ * getrec() replacement * ************************/ #include /* FIXME: it would be better to drop this dependency... */ #include "kseq.h" KSEQ_INIT2(, gzFile, gzread) static gzFile g_fp; static kseq_t *g_kseq; static int g_firsttime = 1, g_is_stdin = 0; static kstring_t g_str; int bio_getrec(char **pbuf, int *psize, int isrecord) { extern Awkfloat *ARGC; extern int argno, recsize; extern char *file; extern Cell **fldtab; int i, c, saveb0, dret, bufsize = *psize, savesize = *psize; char *p, *buf = *pbuf; if (g_firsttime) { /* mimicing initgetrec() in lib.c */ g_firsttime = 0; for (i = 1; i < *ARGC; i++) { p = getargv(i); /* find 1st real filename */ if (p == NULL || *p == '\0') { /* deleted or zapped */ argno++; continue; } if (!isclvar(p)) { setsval(lookup("FILENAME", symtab), p); goto getrec_start; } setclvar(p); /* a commandline assignment before filename */ argno++; } g_fp = gzdopen(fileno(stdin), "r"); /* no filenames, so use stdin */ g_kseq = kseq_init(g_fp); g_is_stdin = 1; } getrec_start: if (isrecord) { donefld = 0; /* these are defined in lib.c */ donerec = 1; } saveb0 = buf[0]; buf[0] = 0; /* this is effective at the end of file */ while (argno < *ARGC || g_is_stdin) { if (g_kseq == 0) { /* have to open a new file */ file = getargv(argno); if (file == NULL || *file == '\0') { /* deleted or zapped */ argno++; continue; } if (isclvar(file)) { /* a var=value arg */ setclvar(file); argno++; continue; } *FILENAME = file; if (*file == '-' && *(file+1) == '\0') { g_fp = gzdopen(fileno(stdin), "r"); g_kseq = kseq_init(g_fp); g_is_stdin = 1; } else { if ((g_fp = gzopen(file, "r")) == NULL) FATAL("can't open file %s", file); g_kseq = kseq_init(g_fp); g_is_stdin = 0; } setfval(fnrloc, 0.0); } if (bio_fmt != BIO_FASTX) { c = ks_getuntil(g_kseq->f, **RS, &g_str, &dret); } else { c = kseq_read(g_kseq); if (c >= 0) { g_str.l = 0; g_str.m = g_kseq->name.l + g_kseq->comment.l + g_kseq->seq.l + g_kseq->qual.l + 4; kroundup32(g_str.m); g_str.s = (char*)realloc(g_str.s, g_str.m); for (i = 0; i < g_kseq->name.l; ++i) g_str.s[g_str.l++] = g_kseq->name.s[i]; g_str.s[g_str.l++] = '\t'; for (i = 0; i < g_kseq->seq.l; ++i) g_str.s[g_str.l++] = g_kseq->seq.s[i]; g_str.s[g_str.l++] = '\t'; for (i = 0; i < g_kseq->qual.l; ++i) g_str.s[g_str.l++] = g_kseq->qual.s[i]; g_str.s[g_str.l++] = '\t'; for (i = 0; i < g_kseq->comment.l; ++i) g_str.s[g_str.l++] = g_kseq->comment.s[i]; g_str.s[g_str.l++] = '\0'; } else { g_str.l = 0; if (g_str.s) g_str.s[0] = '\0'; } } adjbuf(&buf, &bufsize, g_str.l + 1, recsize, 0, "bio_getrec"); memcpy(buf, g_str.s, g_str.l + 1); if (c >= 0) { /* normal record */ if (isrecord) { if (freeable(fldtab[0])) xfree(fldtab[0]->sval); fldtab[0]->sval = buf; /* buf == record */ fldtab[0]->tval = REC | STR | DONTFREE; if (is_number(fldtab[0]->sval)) { fldtab[0]->fval = atof(fldtab[0]->sval); fldtab[0]->tval |= NUM; } } setfval(nrloc, nrloc->fval+1); setfval(fnrloc, fnrloc->fval+1); *pbuf = buf; *psize = bufsize; return 1; } /* EOF arrived on this file; set up next */ if (!g_is_stdin) { kseq_destroy(g_kseq); gzclose(g_fp); } g_fp = 0; g_kseq = 0; g_is_stdin = 0; argno++; } buf[0] = saveb0; *pbuf = buf; *psize = savesize; return 0; /* true end of file */ } bioawk-1.0/addon.h000066400000000000000000000025331220715177100140720ustar00rootroot00000000000000#ifndef ADDON_H #define ADDON_H /* do not change these values, as they are tied to col_def[][] in addon.c */ #define BIO_NULL -1 #define BIO_HDR 0 #define BIO_BED 1 #define BIO_SAM 2 #define BIO_VCF 3 #define BIO_GFF 4 #define BIO_FASTX 5 #define BIO_SHOW_HDR 0x1 extern int bio_fmt, bio_flag; extern char *bio_hdr_chr; int bio_get_fmt(const char *s); int bio_skip_hdr(const char *r); void bio_set_colnm(void); int bio_getrec(char **pbuf, int *psize, int isrecord); /* The following explains how to add a new function. 1) Add a function index * (e.g. #define BIO_FFOO 102) in addon.h. The integer index must be larger than * 14 in the current awk implementation (see also macros starting with "F" * defined in awk.h). 2) Add the function name and the function index in the * keywords array defined in lex.c. Remember to keep the array sorted. 3) * Implement the actual function in bio_func(). */ #define BIO_FAND 101 #define BIO_FOR 102 #define BIO_FXOR 103 #define BIO_FLSHIFT 104 /* to add */ #define BIO_FRSHIFT 105 /* to add */ #define BIO_FCOMPL 106 /* to add */ #define BIO_FREVERSE 201 #define BIO_FREVCOMP 202 #define BIO_FGC 203 #define BIO_FMEANQUAL 204 #define BIO_FQUALCOUNT 205 #define BIO_FTRIMQ 206 struct Cell; struct Node; struct Cell *bio_func(int f, struct Cell *x, struct Node **a); #endif bioawk-1.0/awk.1000066400000000000000000000273171220715177100135070ustar00rootroot00000000000000.de EX .nf .ft CW .. .de EE .br .fi .ft 1 .. awk .TH AWK 1 .CT 1 files prog_other .SH NAME awk \- pattern-directed scanning and processing language .SH SYNOPSIS .B awk [ .BI \-F .I fs ] [ .BI \-v .I var=value ] [ .I 'prog' | .BI \-f .I progfile ] [ .I file ... ] .SH DESCRIPTION .I Awk scans each input .I file for lines that match any of a set of patterns specified literally in .IR prog or in one or more files specified as .B \-f .IR progfile . With each pattern there can be an associated action that will be performed when a line of a .I file matches the pattern. Each line is matched against the pattern portion of every pattern-action statement; the associated action is performed for each matched pattern. The file name .B \- means the standard input. Any .IR file of the form .I var=value is treated as an assignment, not a filename, and is executed at the time it would have been opened if it were a filename. The option .B \-v followed by .I var=value is an assignment to be done before .I prog is executed; any number of .B \-v options may be present. The .B \-F .IR fs option defines the input field separator to be the regular expression .IR fs. .PP An input line is normally made up of fields separated by white space, or by regular expression .BR FS . The fields are denoted .BR $1 , .BR $2 , \&..., while .B $0 refers to the entire line. If .BR FS is null, the input line is split into one field per character. .PP A pattern-action statement has the form .IP .IB pattern " { " action " } .PP A missing .BI { " action " } means print the line; a missing pattern always matches. Pattern-action statements are separated by newlines or semicolons. .PP An action is a sequence of statements. A statement can be one of the following: .PP .EX .ta \w'\f(CWdelete array[expression]'u .RS .nf .ft CW if(\fI expression \fP)\fI statement \fP\fR[ \fPelse\fI statement \fP\fR]\fP while(\fI expression \fP)\fI statement\fP for(\fI expression \fP;\fI expression \fP;\fI expression \fP)\fI statement\fP for(\fI var \fPin\fI array \fP)\fI statement\fP do\fI statement \fPwhile(\fI expression \fP) break continue {\fR [\fP\fI statement ... \fP\fR] \fP} \fIexpression\fP #\fR commonly\fP\fI var = expression\fP print\fR [ \fP\fIexpression-list \fP\fR] \fP\fR[ \fP>\fI expression \fP\fR]\fP printf\fI format \fP\fR[ \fP,\fI expression-list \fP\fR] \fP\fR[ \fP>\fI expression \fP\fR]\fP return\fR [ \fP\fIexpression \fP\fR]\fP next #\fR skip remaining patterns on this input line\fP nextfile #\fR skip rest of this file, open next, start at top\fP delete\fI array\fP[\fI expression \fP] #\fR delete an array element\fP delete\fI array\fP #\fR delete all elements of array\fP exit\fR [ \fP\fIexpression \fP\fR]\fP #\fR exit immediately; status is \fP\fIexpression\fP .fi .RE .EE .DT .PP Statements are terminated by semicolons, newlines or right braces. An empty .I expression-list stands for .BR $0 . String constants are quoted \&\f(CW"\ "\fR, with the usual C escapes recognized within. Expressions take on string or numeric values as appropriate, and are built using the operators .B + \- * / % ^ (exponentiation), and concatenation (indicated by white space). The operators .B ! ++ \-\- += \-= *= /= %= ^= > >= < <= == != ?: are also available in expressions. Variables may be scalars, array elements (denoted .IB x [ i ] ) or fields. Variables are initialized to the null string. Array subscripts may be any string, not necessarily numeric; this allows for a form of associative memory. Multiple subscripts such as .B [i,j,k] are permitted; the constituents are concatenated, separated by the value of .BR SUBSEP . .PP The .B print statement prints its arguments on the standard output (or on a file if .BI > file or .BI >> file is present or on a pipe if .BI | cmd is present), separated by the current output field separator, and terminated by the output record separator. .I file and .I cmd may be literal names or parenthesized expressions; identical string values in different statements denote the same open file. The .B printf statement formats its expression list according to the format (see .IR printf (3)) . The built-in function .BI close( expr ) closes the file or pipe .IR expr . The built-in function .BI fflush( expr ) flushes any buffered output for the file or pipe .IR expr . .PP The mathematical functions .BR exp , .BR log , .BR sqrt , .BR sin , .BR cos , and .BR atan2 are built in. Other built-in functions: .TF length .TP .B length the length of its argument taken as a string, or of .B $0 if no argument. .TP .B rand random number on (0,1) .TP .B srand sets seed for .B rand and returns the previous seed. .TP .B int truncates to an integer value .TP .BI substr( s , " m" , " n\fB) the .IR n -character substring of .I s that begins at position .IR m counted from 1. .TP .BI index( s , " t" ) the position in .I s where the string .I t occurs, or 0 if it does not. .TP .BI match( s , " r" ) the position in .I s where the regular expression .I r occurs, or 0 if it does not. The variables .B RSTART and .B RLENGTH are set to the position and length of the matched string. .TP .BI split( s , " a" , " fs\fB) splits the string .I s into array elements .IB a [1] , .IB a [2] , \&..., .IB a [ n ] , and returns .IR n . The separation is done with the regular expression .I fs or with the field separator .B FS if .I fs is not given. An empty string as field separator splits the string into one array element per character. .TP .BI sub( r , " t" , " s\fB) substitutes .I t for the first occurrence of the regular expression .I r in the string .IR s . If .I s is not given, .B $0 is used. .TP .B gsub same as .B sub except that all occurrences of the regular expression are replaced; .B sub and .B gsub return the number of replacements. .TP .BI sprintf( fmt , " expr" , " ...\fB ) the string resulting from formatting .I expr ... according to the .IR printf (3) format .I fmt .TP .BI system( cmd ) executes .I cmd and returns its exit status .TP .BI tolower( str ) returns a copy of .I str with all upper-case characters translated to their corresponding lower-case equivalents. .TP .BI toupper( str ) returns a copy of .I str with all lower-case characters translated to their corresponding upper-case equivalents. .PD .PP The ``function'' .B getline sets .B $0 to the next input record from the current input file; .B getline .BI < file sets .B $0 to the next record from .IR file . .B getline .I x sets variable .I x instead. Finally, .IB cmd " | getline pipes the output of .I cmd into .BR getline ; each call of .B getline returns the next line of output from .IR cmd . In all cases, .B getline returns 1 for a successful input, 0 for end of file, and \-1 for an error. .PP Patterns are arbitrary Boolean combinations (with .BR "! || &&" ) of regular expressions and relational expressions. Regular expressions are as in .IR egrep ; see .IR grep (1). Isolated regular expressions in a pattern apply to the entire line. Regular expressions may also occur in relational expressions, using the operators .BR ~ and .BR !~ . .BI / re / is a constant regular expression; any string (constant or variable) may be used as a regular expression, except in the position of an isolated regular expression in a pattern. .PP A pattern may consist of two patterns separated by a comma; in this case, the action is performed for all lines from an occurrence of the first pattern though an occurrence of the second. .PP A relational expression is one of the following: .IP .I expression matchop regular-expression .br .I expression relop expression .br .IB expression " in " array-name .br .BI ( expr , expr,... ") in " array-name .PP where a relop is any of the six relational operators in C, and a matchop is either .B ~ (matches) or .B !~ (does not match). A conditional is an arithmetic expression, a relational expression, or a Boolean combination of these. .PP The special patterns .B BEGIN and .B END may be used to capture control before the first input line is read and after the last. .B BEGIN and .B END do not combine with other patterns. .PP Variable names with special meanings: .TF FILENAME .TP .B CONVFMT conversion format used when converting numbers (default .BR "%.6g" ) .TP .B FS regular expression used to separate fields; also settable by option .BI \-F fs. .TP .BR NF number of fields in the current record .TP .B NR ordinal number of the current record .TP .B FNR ordinal number of the current record in the current file .TP .B FILENAME the name of the current input file .TP .B RS input record separator (default newline) .TP .B OFS output field separator (default blank) .TP .B ORS output record separator (default newline) .TP .B OFMT output format for numbers (default .BR "%.6g" ) .TP .B SUBSEP separates multiple subscripts (default 034) .TP .B ARGC argument count, assignable .TP .B ARGV argument array, assignable; non-null members are taken as filenames .TP .B ENVIRON array of environment variables; subscripts are names. .PD .PP Functions may be defined (at the position of a pattern-action statement) thus: .IP .B function foo(a, b, c) { ...; return x } .PP Parameters are passed by value if scalar and by reference if array name; functions may be called recursively. Parameters are local to the function; all other variables are global. Thus local variables may be created by providing excess parameters in the function definition. .SH EXAMPLES .TP .EX length($0) > 72 .EE Print lines longer than 72 characters. .TP .EX { print $2, $1 } .EE Print first two fields in opposite order. .PP .EX BEGIN { FS = ",[ \et]*|[ \et]+" } { print $2, $1 } .EE .ns .IP Same, with input fields separated by comma and/or blanks and tabs. .PP .EX .nf { s += $1 } END { print "sum is", s, " average is", s/NR } .fi .EE .ns .IP Add up first column, print sum and average. .TP .EX /start/, /stop/ .EE Print all lines between start/stop pairs. .PP .EX .nf BEGIN { # Simulate echo(1) for (i = 1; i < ARGC; i++) printf "%s ", ARGV[i] printf "\en" exit } .fi .EE .SH BIOAWK EXTENSIONS .PP Bioawk adds a new .B \-c .IR fmt option that specifies the input format. The behavior of bioawk may vary depending on the value of .IR fmt . When .I fmt is .IR header " or " hdr , bioawk parses named columns. It automatically adds variables whose names are taken from the first line and values from the column index. Special characters are converted to a underscore. When .I fmt is .IR sam , " vcf" , " bed " or " gff" , it sets predefined column names. Users may check out the predefined column names by .B -c .IR help . When .I fmt is .IR fastx , bioawk will parse the input FASTA or FASTQ file into a TAB-delimited format first with each line consisting of sequence name, sequence, quality and comments, and then sets column names. Note that when .B -c .I fmt is in use, the input file can be optionally gzip'ed. .PP Bioawk also adds more built-in functions: .TF length .TP .BI reverse( s ) reverse string .I s .TP .BI revcomp( s ) reverse complement a nucleotide string .I s in the IUB encoding. .TP .BI trimq( qual , " beg" , " end" , " param" ) trim quality string .I qual in the Sanger scale using Richard Mott's algorithm (used in Phred). The 0-based beginning and ending positions are written to .IR beg " and " end , respectively. The last arguement .I param is the single parameter used in the algorithm, which is optional and defaults 0.05. .TP .BI and( x , " y" ) bit AND operation (& in C) .TP .BI or( x , " y" ) bit OR operation (| in C) .TP .BI xor( x , " y" ) bit XOR operation (^ in C) .SH SEE ALSO .IR lex (1), .IR sed (1) .br A. V. Aho, B. W. Kernighan, P. J. Weinberger, .I The AWK Programming Language, Addison-Wesley, 1988. ISBN 0-201-07981-X .SH BUGS There are no explicit conversions between numbers and strings. To force an expression to be treated as a number add 0 to it; to force it to be treated as a string concatenate \&\f(CW""\fP to it. .br The scope rules for variables in functions are a botch; the syntax is worse. bioawk-1.0/awk.h000066400000000000000000000145121220715177100135670ustar00rootroot00000000000000/**************************************************************** Copyright (C) Lucent Technologies 1997 All Rights Reserved Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that the copyright notice and this permission notice and warranty disclaimer appear in supporting documentation, and that the name Lucent Technologies or any of its entities not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ****************************************************************/ #include #include "addon.h" typedef double Awkfloat; /* unsigned char is more trouble than it's worth */ typedef unsigned char uschar; #define xfree(a) { if ((a) != NULL) { free((void *) (a)); (a) = NULL; } } #define NN(p) ((p) ? (p) : "(null)") /* guaranteed non-null for dprintf */ #define DEBUG #ifdef DEBUG /* uses have to be doubly parenthesized */ # define dprintf(x) if (dbg) printf x #else # define dprintf(x) #endif #define DEFAULT_FS " " extern int compile_time; /* 1 if compiling, 0 if running */ extern int safe; /* 0 => unsafe, 1 => safe */ #define RECSIZE (8 * 1024) /* sets limit on records, fields, etc., etc. */ extern int recsize; /* size of current record, orig RECSIZE */ extern char **FS; extern char **RS; extern char **ORS; extern char **OFS; extern char **OFMT; extern Awkfloat *NR; extern Awkfloat *FNR; extern Awkfloat *NF; extern char **FILENAME; extern char **SUBSEP; extern Awkfloat *RSTART; extern Awkfloat *RLENGTH; extern char *record; /* points to $0 */ extern int lineno; /* line number in awk program */ extern int errorflag; /* 1 if error has occurred */ extern int donefld; /* 1 if record broken into fields */ extern int donerec; /* 1 if record is valid (no fld has changed */ extern char inputFS[]; /* FS at time of input, for field splitting */ extern int dbg; extern char *patbeg; /* beginning of pattern matched */ extern int patlen; /* length of pattern matched. set in b.c */ /* Cell: all information about a variable or constant */ typedef struct Cell { uschar ctype; /* OCELL, OBOOL, OJUMP, etc. */ uschar csub; /* CCON, CTEMP, CFLD, etc. */ char *nval; /* name, for variables only */ char *sval; /* string value */ Awkfloat fval; /* value as number */ int tval; /* type info: STR|NUM|ARR|FCN|FLD|CON|DONTFREE */ struct Cell *cnext; /* ptr to next if chained */ } Cell; typedef struct Array { /* symbol table array */ int nelem; /* elements in table right now */ int size; /* size of tab */ Cell **tab; /* hash table pointers */ } Array; #define NSYMTAB 50 /* initial size of a symbol table */ extern Array *symtab; extern Cell *nrloc; /* NR */ extern Cell *fnrloc; /* FNR */ extern Cell *nfloc; /* NF */ extern Cell *rstartloc; /* RSTART */ extern Cell *rlengthloc; /* RLENGTH */ /* Cell.tval values: */ #define NUM 01 /* number value is valid */ #define STR 02 /* string value is valid */ #define DONTFREE 04 /* string space is not freeable */ #define CON 010 /* this is a constant */ #define ARR 020 /* this is an array */ #define FCN 040 /* this is a function name */ #define FLD 0100 /* this is a field $1, $2, ... */ #define REC 0200 /* this is $0 */ /* function types */ #define FLENGTH 1 #define FSQRT 2 #define FEXP 3 #define FLOG 4 #define FINT 5 #define FSYSTEM 6 #define FRAND 7 #define FSRAND 8 #define FSIN 9 #define FCOS 10 #define FATAN 11 #define FTOUPPER 12 #define FTOLOWER 13 #define FFLUSH 14 /* Node: parse tree is made of nodes, with Cell's at bottom */ typedef struct Node { int ntype; struct Node *nnext; int lineno; int nobj; struct Node *narg[1]; /* variable: actual size set by calling malloc */ } Node; #define NIL ((Node *) 0) extern Node *winner; extern Node *nullstat; extern Node *nullnode; /* ctypes */ #define OCELL 1 #define OBOOL 2 #define OJUMP 3 /* Cell subtypes: csub */ #define CFREE 7 #define CCOPY 6 #define CCON 5 #define CTEMP 4 #define CNAME 3 #define CVAR 2 #define CFLD 1 #define CUNK 0 /* bool subtypes */ #define BTRUE 11 #define BFALSE 12 /* jump subtypes */ #define JEXIT 21 #define JNEXT 22 #define JBREAK 23 #define JCONT 24 #define JRET 25 #define JNEXTFILE 26 /* node types */ #define NVALUE 1 #define NSTAT 2 #define NEXPR 3 extern int pairstack[], paircnt; #define notlegal(n) (n <= FIRSTTOKEN || n >= LASTTOKEN || proctab[n-FIRSTTOKEN] == nullproc) #define isvalue(n) ((n)->ntype == NVALUE) #define isexpr(n) ((n)->ntype == NEXPR) #define isjump(n) ((n)->ctype == OJUMP) #define isexit(n) ((n)->csub == JEXIT) #define isbreak(n) ((n)->csub == JBREAK) #define iscont(n) ((n)->csub == JCONT) #define isnext(n) ((n)->csub == JNEXT || (n)->csub == JNEXTFILE) #define isret(n) ((n)->csub == JRET) #define isrec(n) ((n)->tval & REC) #define isfld(n) ((n)->tval & FLD) #define isstr(n) ((n)->tval & STR) #define isnum(n) ((n)->tval & NUM) #define isarr(n) ((n)->tval & ARR) #define isfcn(n) ((n)->tval & FCN) #define istrue(n) ((n)->csub == BTRUE) #define istemp(n) ((n)->csub == CTEMP) #define isargument(n) ((n)->nobj == ARG) /* #define freeable(p) (!((p)->tval & DONTFREE)) */ #define freeable(p) ( ((p)->tval & (STR|DONTFREE)) == STR ) /* structures used by regular expression matching machinery, mostly b.c: */ #define NCHARS (256+3) /* 256 handles 8-bit chars; 128 does 7-bit */ /* watch out in match(), etc. */ #define NSTATES 32 typedef struct rrow { long ltype; /* long avoids pointer warnings on 64-bit */ union { int i; Node *np; uschar *up; } lval; /* because Al stores a pointer in it! */ int *lfollow; } rrow; typedef struct fa { uschar gototab[NSTATES][NCHARS]; uschar out[NSTATES]; uschar *restr; int *posns[NSTATES]; int anchor; int use; int initstat; int curstat; int accept; int reset; struct rrow re[1]; /* variable: actual size set by calling malloc */ } fa; #include "proto.h" bioawk-1.0/awkgram.y000066400000000000000000000331321220715177100144560ustar00rootroot00000000000000/**************************************************************** Copyright (C) Lucent Technologies 1997 All Rights Reserved Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that the copyright notice and this permission notice and warranty disclaimer appear in supporting documentation, and that the name Lucent Technologies or any of its entities not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ****************************************************************/ %{ #include #include #include "awk.h" void checkdup(Node *list, Cell *item); int yywrap(void) { return(1); } Node *beginloc = 0; Node *endloc = 0; int infunc = 0; /* = 1 if in arglist or body of func */ int inloop = 0; /* = 1 if in while, for, do */ char *curfname = 0; /* current function name */ Node *arglist = 0; /* list of args for current function */ %} %union { Node *p; Cell *cp; int i; char *s; } %token FIRSTTOKEN /* must be first */ %token

PROGRAM PASTAT PASTAT2 XBEGIN XEND %token NL ',' '{' '(' '|' ';' '/' ')' '}' '[' ']' %token ARRAY %token MATCH NOTMATCH MATCHOP %token FINAL DOT ALL CCL NCCL CHAR OR STAR QUEST PLUS EMPTYRE %token AND BOR APPEND EQ GE GT LE LT NE IN %token ARG BLTIN BREAK CLOSE CONTINUE DELETE DO EXIT FOR FUNC %token SUB GSUB IF INDEX LSUBSTR MATCHFCN NEXT NEXTFILE %token ADD MINUS MULT DIVIDE MOD %token ASSIGN ASGNOP ADDEQ SUBEQ MULTEQ DIVEQ MODEQ POWEQ %token PRINT PRINTF SPRINTF %token

ELSE INTEST CONDEXPR %token POSTINCR PREINCR POSTDECR PREDECR %token VAR IVAR VARNF CALL NUMBER STRING %token REGEXPR %type

pas pattern ppattern plist pplist patlist prarg term re %type

pa_pat pa_stat pa_stats %type reg_expr %type

simple_stmt opt_simple_stmt stmt stmtlist %type

var varname funcname varlist %type

for if else while %type do st %type pst opt_pst lbrace rbrace rparen comma nl opt_nl and bor %type subop print %right ASGNOP %right '?' %right ':' %left BOR %left AND %left GETLINE %nonassoc APPEND EQ GE GT LE LT NE MATCHOP IN '|' %left ARG BLTIN BREAK CALL CLOSE CONTINUE DELETE DO EXIT FOR FUNC %left GSUB IF INDEX LSUBSTR MATCHFCN NEXT NUMBER %left PRINT PRINTF RETURN SPLIT SPRINTF STRING SUB SUBSTR %left REGEXPR VAR VARNF IVAR WHILE '(' %left CAT %left '+' '-' %left '*' '/' '%' %left NOT UMINUS %right POWER %right DECR INCR %left INDIRECT %token LASTTOKEN /* must be last */ %% program: pas { if (errorflag==0) winner = (Node *)stat3(PROGRAM, beginloc, $1, endloc); } | error { yyclearin; bracecheck(); SYNTAX("bailing out"); } ; and: AND | and NL ; bor: BOR | bor NL ; comma: ',' | comma NL ; do: DO | do NL ; else: ELSE | else NL ; for: FOR '(' opt_simple_stmt ';' opt_nl pattern ';' opt_nl opt_simple_stmt rparen {inloop++;} stmt { --inloop; $$ = stat4(FOR, $3, notnull($6), $9, $12); } | FOR '(' opt_simple_stmt ';' ';' opt_nl opt_simple_stmt rparen {inloop++;} stmt { --inloop; $$ = stat4(FOR, $3, NIL, $7, $10); } | FOR '(' varname IN varname rparen {inloop++;} stmt { --inloop; $$ = stat3(IN, $3, makearr($5), $8); } ; funcname: VAR { setfname($1); } | CALL { setfname($1); } ; if: IF '(' pattern rparen { $$ = notnull($3); } ; lbrace: '{' | lbrace NL ; nl: NL | nl NL ; opt_nl: /* empty */ { $$ = 0; } | nl ; opt_pst: /* empty */ { $$ = 0; } | pst ; opt_simple_stmt: /* empty */ { $$ = 0; } | simple_stmt ; pas: opt_pst { $$ = 0; } | opt_pst pa_stats opt_pst { $$ = $2; } ; pa_pat: pattern { $$ = notnull($1); } ; pa_stat: pa_pat { $$ = stat2(PASTAT, $1, stat2(PRINT, rectonode(), NIL)); } | pa_pat lbrace stmtlist '}' { $$ = stat2(PASTAT, $1, $3); } | pa_pat ',' opt_nl pa_pat { $$ = pa2stat($1, $4, stat2(PRINT, rectonode(), NIL)); } | pa_pat ',' opt_nl pa_pat lbrace stmtlist '}' { $$ = pa2stat($1, $4, $6); } | lbrace stmtlist '}' { $$ = stat2(PASTAT, NIL, $2); } | XBEGIN lbrace stmtlist '}' { beginloc = linkum(beginloc, $3); $$ = 0; } | XEND lbrace stmtlist '}' { endloc = linkum(endloc, $3); $$ = 0; } | FUNC funcname '(' varlist rparen {infunc++;} lbrace stmtlist '}' { infunc--; curfname=0; defn((Cell *)$2, $4, $8); $$ = 0; } ; pa_stats: pa_stat | pa_stats opt_pst pa_stat { $$ = linkum($1, $3); } ; patlist: pattern | patlist comma pattern { $$ = linkum($1, $3); } ; ppattern: var ASGNOP ppattern { $$ = op2($2, $1, $3); } | ppattern '?' ppattern ':' ppattern %prec '?' { $$ = op3(CONDEXPR, notnull($1), $3, $5); } | ppattern bor ppattern %prec BOR { $$ = op2(BOR, notnull($1), notnull($3)); } | ppattern and ppattern %prec AND { $$ = op2(AND, notnull($1), notnull($3)); } | ppattern MATCHOP reg_expr { $$ = op3($2, NIL, $1, (Node*)makedfa($3, 0)); } | ppattern MATCHOP ppattern { if (constnode($3)) $$ = op3($2, NIL, $1, (Node*)makedfa(strnode($3), 0)); else $$ = op3($2, (Node *)1, $1, $3); } | ppattern IN varname { $$ = op2(INTEST, $1, makearr($3)); } | '(' plist ')' IN varname { $$ = op2(INTEST, $2, makearr($5)); } | ppattern term %prec CAT { $$ = op2(CAT, $1, $2); } | re | term ; pattern: var ASGNOP pattern { $$ = op2($2, $1, $3); } | pattern '?' pattern ':' pattern %prec '?' { $$ = op3(CONDEXPR, notnull($1), $3, $5); } | pattern bor pattern %prec BOR { $$ = op2(BOR, notnull($1), notnull($3)); } | pattern and pattern %prec AND { $$ = op2(AND, notnull($1), notnull($3)); } | pattern EQ pattern { $$ = op2($2, $1, $3); } | pattern GE pattern { $$ = op2($2, $1, $3); } | pattern GT pattern { $$ = op2($2, $1, $3); } | pattern LE pattern { $$ = op2($2, $1, $3); } | pattern LT pattern { $$ = op2($2, $1, $3); } | pattern NE pattern { $$ = op2($2, $1, $3); } | pattern MATCHOP reg_expr { $$ = op3($2, NIL, $1, (Node*)makedfa($3, 0)); } | pattern MATCHOP pattern { if (constnode($3)) $$ = op3($2, NIL, $1, (Node*)makedfa(strnode($3), 0)); else $$ = op3($2, (Node *)1, $1, $3); } | pattern IN varname { $$ = op2(INTEST, $1, makearr($3)); } | '(' plist ')' IN varname { $$ = op2(INTEST, $2, makearr($5)); } | pattern '|' GETLINE var { if (safe) SYNTAX("cmd | getline is unsafe"); else $$ = op3(GETLINE, $4, itonp($2), $1); } | pattern '|' GETLINE { if (safe) SYNTAX("cmd | getline is unsafe"); else $$ = op3(GETLINE, (Node*)0, itonp($2), $1); } | pattern term %prec CAT { $$ = op2(CAT, $1, $2); } | re | term ; plist: pattern comma pattern { $$ = linkum($1, $3); } | plist comma pattern { $$ = linkum($1, $3); } ; pplist: ppattern | pplist comma ppattern { $$ = linkum($1, $3); } ; prarg: /* empty */ { $$ = rectonode(); } | pplist | '(' plist ')' { $$ = $2; } ; print: PRINT | PRINTF ; pst: NL | ';' | pst NL | pst ';' ; rbrace: '}' | rbrace NL ; re: reg_expr { $$ = op3(MATCH, NIL, rectonode(), (Node*)makedfa($1, 0)); } | NOT re { $$ = op1(NOT, notnull($2)); } ; reg_expr: '/' {startreg();} REGEXPR '/' { $$ = $3; } ; rparen: ')' | rparen NL ; simple_stmt: print prarg '|' term { if (safe) SYNTAX("print | is unsafe"); else $$ = stat3($1, $2, itonp($3), $4); } | print prarg APPEND term { if (safe) SYNTAX("print >> is unsafe"); else $$ = stat3($1, $2, itonp($3), $4); } | print prarg GT term { if (safe) SYNTAX("print > is unsafe"); else $$ = stat3($1, $2, itonp($3), $4); } | print prarg { $$ = stat3($1, $2, NIL, NIL); } | DELETE varname '[' patlist ']' { $$ = stat2(DELETE, makearr($2), $4); } | DELETE varname { $$ = stat2(DELETE, makearr($2), 0); } | pattern { $$ = exptostat($1); } | error { yyclearin; SYNTAX("illegal statement"); } ; st: nl | ';' opt_nl ; stmt: BREAK st { if (!inloop) SYNTAX("break illegal outside of loops"); $$ = stat1(BREAK, NIL); } | CONTINUE st { if (!inloop) SYNTAX("continue illegal outside of loops"); $$ = stat1(CONTINUE, NIL); } | do {inloop++;} stmt {--inloop;} WHILE '(' pattern ')' st { $$ = stat2(DO, $3, notnull($7)); } | EXIT pattern st { $$ = stat1(EXIT, $2); } | EXIT st { $$ = stat1(EXIT, NIL); } | for | if stmt else stmt { $$ = stat3(IF, $1, $2, $4); } | if stmt { $$ = stat3(IF, $1, $2, NIL); } | lbrace stmtlist rbrace { $$ = $2; } | NEXT st { if (infunc) SYNTAX("next is illegal inside a function"); $$ = stat1(NEXT, NIL); } | NEXTFILE st { if (infunc) SYNTAX("nextfile is illegal inside a function"); $$ = stat1(NEXTFILE, NIL); } | RETURN pattern st { $$ = stat1(RETURN, $2); } | RETURN st { $$ = stat1(RETURN, NIL); } | simple_stmt st | while {inloop++;} stmt { --inloop; $$ = stat2(WHILE, $1, $3); } | ';' opt_nl { $$ = 0; } ; stmtlist: stmt | stmtlist stmt { $$ = linkum($1, $2); } ; subop: SUB | GSUB ; term: term '/' ASGNOP term { $$ = op2(DIVEQ, $1, $4); } | term '+' term { $$ = op2(ADD, $1, $3); } | term '-' term { $$ = op2(MINUS, $1, $3); } | term '*' term { $$ = op2(MULT, $1, $3); } | term '/' term { $$ = op2(DIVIDE, $1, $3); } | term '%' term { $$ = op2(MOD, $1, $3); } | term POWER term { $$ = op2(POWER, $1, $3); } | '-' term %prec UMINUS { $$ = op1(UMINUS, $2); } | '+' term %prec UMINUS { $$ = $2; } | NOT term %prec UMINUS { $$ = op1(NOT, notnull($2)); } | BLTIN '(' ')' { $$ = op2(BLTIN, itonp($1), rectonode()); } | BLTIN '(' patlist ')' { $$ = op2(BLTIN, itonp($1), $3); } | BLTIN { $$ = op2(BLTIN, itonp($1), rectonode()); } | CALL '(' ')' { $$ = op2(CALL, celltonode($1,CVAR), NIL); } | CALL '(' patlist ')' { $$ = op2(CALL, celltonode($1,CVAR), $3); } | CLOSE term { $$ = op1(CLOSE, $2); } | DECR var { $$ = op1(PREDECR, $2); } | INCR var { $$ = op1(PREINCR, $2); } | var DECR { $$ = op1(POSTDECR, $1); } | var INCR { $$ = op1(POSTINCR, $1); } | GETLINE var LT term { $$ = op3(GETLINE, $2, itonp($3), $4); } | GETLINE LT term { $$ = op3(GETLINE, NIL, itonp($2), $3); } | GETLINE var { $$ = op3(GETLINE, $2, NIL, NIL); } | GETLINE { $$ = op3(GETLINE, NIL, NIL, NIL); } | INDEX '(' pattern comma pattern ')' { $$ = op2(INDEX, $3, $5); } | INDEX '(' pattern comma reg_expr ')' { SYNTAX("index() doesn't permit regular expressions"); $$ = op2(INDEX, $3, (Node*)$5); } | '(' pattern ')' { $$ = $2; } | MATCHFCN '(' pattern comma reg_expr ')' { $$ = op3(MATCHFCN, NIL, $3, (Node*)makedfa($5, 1)); } | MATCHFCN '(' pattern comma pattern ')' { if (constnode($5)) $$ = op3(MATCHFCN, NIL, $3, (Node*)makedfa(strnode($5), 1)); else $$ = op3(MATCHFCN, (Node *)1, $3, $5); } | NUMBER { $$ = celltonode($1, CCON); } | SPLIT '(' pattern comma varname comma pattern ')' /* string */ { $$ = op4(SPLIT, $3, makearr($5), $7, (Node*)STRING); } | SPLIT '(' pattern comma varname comma reg_expr ')' /* const /regexp/ */ { $$ = op4(SPLIT, $3, makearr($5), (Node*)makedfa($7, 1), (Node *)REGEXPR); } | SPLIT '(' pattern comma varname ')' { $$ = op4(SPLIT, $3, makearr($5), NIL, (Node*)STRING); } /* default */ | SPRINTF '(' patlist ')' { $$ = op1($1, $3); } | STRING { $$ = celltonode($1, CCON); } | subop '(' reg_expr comma pattern ')' { $$ = op4($1, NIL, (Node*)makedfa($3, 1), $5, rectonode()); } | subop '(' pattern comma pattern ')' { if (constnode($3)) $$ = op4($1, NIL, (Node*)makedfa(strnode($3), 1), $5, rectonode()); else $$ = op4($1, (Node *)1, $3, $5, rectonode()); } | subop '(' reg_expr comma pattern comma var ')' { $$ = op4($1, NIL, (Node*)makedfa($3, 1), $5, $7); } | subop '(' pattern comma pattern comma var ')' { if (constnode($3)) $$ = op4($1, NIL, (Node*)makedfa(strnode($3), 1), $5, $7); else $$ = op4($1, (Node *)1, $3, $5, $7); } | SUBSTR '(' pattern comma pattern comma pattern ')' { $$ = op3(SUBSTR, $3, $5, $7); } | SUBSTR '(' pattern comma pattern ')' { $$ = op3(SUBSTR, $3, $5, NIL); } | var ; var: varname | varname '[' patlist ']' { $$ = op2(ARRAY, makearr($1), $3); } | IVAR { $$ = op1(INDIRECT, celltonode($1, CVAR)); } | INDIRECT term { $$ = op1(INDIRECT, $2); } ; varlist: /* nothing */ { arglist = $$ = 0; } | VAR { arglist = $$ = celltonode($1,CVAR); } | varlist comma VAR { checkdup($1, $3); arglist = $$ = linkum($1,celltonode($3,CVAR)); } ; varname: VAR { $$ = celltonode($1, CVAR); } | ARG { $$ = op1(ARG, itonp($1)); } | VARNF { $$ = op1(VARNF, (Node *) $1); } ; while: WHILE '(' pattern rparen { $$ = notnull($3); } ; %% void setfname(Cell *p) { if (isarr(p)) SYNTAX("%s is an array, not a function", p->nval); else if (isfcn(p)) SYNTAX("you can't define function %s more than once", p->nval); curfname = p->nval; } int constnode(Node *p) { return isvalue(p) && ((Cell *) (p->narg[0]))->csub == CCON; } char *strnode(Node *p) { return ((Cell *)(p->narg[0]))->sval; } Node *notnull(Node *n) { switch (n->nobj) { case LE: case LT: case EQ: case NE: case GT: case GE: case BOR: case AND: case NOT: return n; default: return op2(NE, n, nullnode); } } void checkdup(Node *vl, Cell *cp) /* check if name already in list */ { char *s = cp->nval; for ( ; vl; vl = vl->nnext) { if (strcmp(s, ((Cell *)(vl->narg[0]))->nval) == 0) { SYNTAX("duplicate argument %s", s); break; } } } bioawk-1.0/b.c000066400000000000000000000545231220715177100132270ustar00rootroot00000000000000/**************************************************************** Copyright (C) Lucent Technologies 1997 All Rights Reserved Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that the copyright notice and this permission notice and warranty disclaimer appear in supporting documentation, and that the name Lucent Technologies or any of its entities not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ****************************************************************/ /* lasciate ogne speranza, voi ch'intrate. */ #define DEBUG #include #include #include #include #include "awk.h" #include "ytab.h" #define HAT (NCHARS+2) /* matches ^ in regular expr */ /* NCHARS is 2**n */ #define MAXLIN 22 #define type(v) (v)->nobj /* badly overloaded here */ #define info(v) (v)->ntype /* badly overloaded here */ #define left(v) (v)->narg[0] #define right(v) (v)->narg[1] #define parent(v) (v)->nnext #define LEAF case CCL: case NCCL: case CHAR: case DOT: case FINAL: case ALL: #define ELEAF case EMPTYRE: /* empty string in regexp */ #define UNARY case STAR: case PLUS: case QUEST: /* encoding in tree Nodes: leaf (CCL, NCCL, CHAR, DOT, FINAL, ALL, EMPTYRE): left is index, right contains value or pointer to value unary (STAR, PLUS, QUEST): left is child, right is null binary (CAT, OR): left and right are children parent contains pointer to parent */ int *setvec; int *tmpset; int maxsetvec = 0; int rtok; /* next token in current re */ int rlxval; static uschar *rlxstr; static uschar *prestr; /* current position in current re */ static uschar *lastre; /* origin of last re */ static int setcnt; static int poscnt; char *patbeg; int patlen; #define NFA 20 /* cache this many dynamic fa's */ fa *fatab[NFA]; int nfatab = 0; /* entries in fatab */ fa *makedfa(const char *s, int anchor) /* returns dfa for reg expr s */ { int i, use, nuse; fa *pfa; static int now = 1; if (setvec == 0) { /* first time through any RE */ maxsetvec = MAXLIN; setvec = (int *) malloc(maxsetvec * sizeof(int)); tmpset = (int *) malloc(maxsetvec * sizeof(int)); if (setvec == 0 || tmpset == 0) overflo("out of space initializing makedfa"); } if (compile_time) /* a constant for sure */ return mkdfa(s, anchor); for (i = 0; i < nfatab; i++) /* is it there already? */ if (fatab[i]->anchor == anchor && strcmp((const char *) fatab[i]->restr, s) == 0) { fatab[i]->use = now++; return fatab[i]; } pfa = mkdfa(s, anchor); if (nfatab < NFA) { /* room for another */ fatab[nfatab] = pfa; fatab[nfatab]->use = now++; nfatab++; return pfa; } use = fatab[0]->use; /* replace least-recently used */ nuse = 0; for (i = 1; i < nfatab; i++) if (fatab[i]->use < use) { use = fatab[i]->use; nuse = i; } freefa(fatab[nuse]); fatab[nuse] = pfa; pfa->use = now++; return pfa; } fa *mkdfa(const char *s, int anchor) /* does the real work of making a dfa */ /* anchor = 1 for anchored matches, else 0 */ { Node *p, *p1; fa *f; p = reparse(s); p1 = op2(CAT, op2(STAR, op2(ALL, NIL, NIL), NIL), p); /* put ALL STAR in front of reg. exp. */ p1 = op2(CAT, p1, op2(FINAL, NIL, NIL)); /* put FINAL after reg. exp. */ poscnt = 0; penter(p1); /* enter parent pointers and leaf indices */ if ((f = (fa *) calloc(1, sizeof(fa) + poscnt*sizeof(rrow))) == NULL) overflo("out of space for fa"); f->accept = poscnt-1; /* penter has computed number of positions in re */ cfoll(f, p1); /* set up follow sets */ freetr(p1); if ((f->posns[0] = (int *) calloc(1, *(f->re[0].lfollow)*sizeof(int))) == NULL) overflo("out of space in makedfa"); if ((f->posns[1] = (int *) calloc(1, sizeof(int))) == NULL) overflo("out of space in makedfa"); *f->posns[1] = 0; f->initstat = makeinit(f, anchor); f->anchor = anchor; f->restr = (uschar *) tostring(s); return f; } int makeinit(fa *f, int anchor) { int i, k; f->curstat = 2; f->out[2] = 0; f->reset = 0; k = *(f->re[0].lfollow); xfree(f->posns[2]); if ((f->posns[2] = (int *) calloc(1, (k+1)*sizeof(int))) == NULL) overflo("out of space in makeinit"); for (i=0; i <= k; i++) { (f->posns[2])[i] = (f->re[0].lfollow)[i]; } if ((f->posns[2])[1] == f->accept) f->out[2] = 1; for (i=0; i < NCHARS; i++) f->gototab[2][i] = 0; f->curstat = cgoto(f, 2, HAT); if (anchor) { *f->posns[2] = k-1; /* leave out position 0 */ for (i=0; i < k; i++) { (f->posns[0])[i] = (f->posns[2])[i]; } f->out[0] = f->out[2]; if (f->curstat != 2) --(*f->posns[f->curstat]); } return f->curstat; } void penter(Node *p) /* set up parent pointers and leaf indices */ { switch (type(p)) { ELEAF LEAF info(p) = poscnt; poscnt++; break; UNARY penter(left(p)); parent(left(p)) = p; break; case CAT: case OR: penter(left(p)); penter(right(p)); parent(left(p)) = p; parent(right(p)) = p; break; default: /* can't happen */ FATAL("can't happen: unknown type %d in penter", type(p)); break; } } void freetr(Node *p) /* free parse tree */ { switch (type(p)) { ELEAF LEAF xfree(p); break; UNARY freetr(left(p)); xfree(p); break; case CAT: case OR: freetr(left(p)); freetr(right(p)); xfree(p); break; default: /* can't happen */ FATAL("can't happen: unknown type %d in freetr", type(p)); break; } } /* in the parsing of regular expressions, metacharacters like . have */ /* to be seen literally; \056 is not a metacharacter. */ int hexstr(uschar **pp) /* find and eval hex string at pp, return new p */ { /* only pick up one 8-bit byte (2 chars) */ uschar *p; int n = 0; int i; for (i = 0, p = (uschar *) *pp; i < 2 && isxdigit(*p); i++, p++) { if (isdigit(*p)) n = 16 * n + *p - '0'; else if (*p >= 'a' && *p <= 'f') n = 16 * n + *p - 'a' + 10; else if (*p >= 'A' && *p <= 'F') n = 16 * n + *p - 'A' + 10; } *pp = (uschar *) p; return n; } #define isoctdigit(c) ((c) >= '0' && (c) <= '7') /* multiple use of arg */ int quoted(uschar **pp) /* pick up next thing after a \\ */ /* and increment *pp */ { uschar *p = *pp; int c; if ((c = *p++) == 't') c = '\t'; else if (c == 'n') c = '\n'; else if (c == 'f') c = '\f'; else if (c == 'r') c = '\r'; else if (c == 'b') c = '\b'; else if (c == '\\') c = '\\'; else if (c == 'x') { /* hexadecimal goo follows */ c = hexstr(&p); /* this adds a null if number is invalid */ } else if (isoctdigit(c)) { /* \d \dd \ddd */ int n = c - '0'; if (isoctdigit(*p)) { n = 8 * n + *p++ - '0'; if (isoctdigit(*p)) n = 8 * n + *p++ - '0'; } c = n; } /* else */ /* c = c; */ *pp = p; return c; } char *cclenter(const char *argp) /* add a character class */ { int i, c, c2; uschar *p = (uschar *) argp; uschar *op, *bp; static uschar *buf = 0; static int bufsz = 100; op = p; if (buf == 0 && (buf = (uschar *) malloc(bufsz)) == NULL) FATAL("out of space for character class [%.10s...] 1", p); bp = buf; for (i = 0; (c = *p++) != 0; ) { if (c == '\\') { c = quoted(&p); } else if (c == '-' && i > 0 && bp[-1] != 0) { if (*p != 0) { c = bp[-1]; c2 = *p++; if (c2 == '\\') c2 = quoted(&p); if (c > c2) { /* empty; ignore */ bp--; i--; continue; } while (c < c2) { if (!adjbuf((char **) &buf, &bufsz, bp-buf+2, 100, (char **) &bp, "cclenter1")) FATAL("out of space for character class [%.10s...] 2", p); *bp++ = ++c; i++; } continue; } } if (!adjbuf((char **) &buf, &bufsz, bp-buf+2, 100, (char **) &bp, "cclenter2")) FATAL("out of space for character class [%.10s...] 3", p); *bp++ = c; i++; } *bp = 0; dprintf( ("cclenter: in = |%s|, out = |%s|\n", op, buf) ); xfree(op); return (char *) tostring((char *) buf); } void overflo(const char *s) { FATAL("regular expression too big: %.30s...", s); } void cfoll(fa *f, Node *v) /* enter follow set of each leaf of vertex v into lfollow[leaf] */ { int i; int *p; switch (type(v)) { ELEAF LEAF f->re[info(v)].ltype = type(v); f->re[info(v)].lval.np = right(v); while (f->accept >= maxsetvec) { /* guessing here! */ maxsetvec *= 4; setvec = (int *) realloc(setvec, maxsetvec * sizeof(int)); tmpset = (int *) realloc(tmpset, maxsetvec * sizeof(int)); if (setvec == 0 || tmpset == 0) overflo("out of space in cfoll()"); } for (i = 0; i <= f->accept; i++) setvec[i] = 0; setcnt = 0; follow(v); /* computes setvec and setcnt */ if ((p = (int *) calloc(1, (setcnt+1)*sizeof(int))) == NULL) overflo("out of space building follow set"); f->re[info(v)].lfollow = p; *p = setcnt; for (i = f->accept; i >= 0; i--) if (setvec[i] == 1) *++p = i; break; UNARY cfoll(f,left(v)); break; case CAT: case OR: cfoll(f,left(v)); cfoll(f,right(v)); break; default: /* can't happen */ FATAL("can't happen: unknown type %d in cfoll", type(v)); } } int first(Node *p) /* collects initially active leaves of p into setvec */ /* returns 0 if p matches empty string */ { int b, lp; switch (type(p)) { ELEAF LEAF lp = info(p); /* look for high-water mark of subscripts */ while (setcnt >= maxsetvec || lp >= maxsetvec) { /* guessing here! */ maxsetvec *= 4; setvec = (int *) realloc(setvec, maxsetvec * sizeof(int)); tmpset = (int *) realloc(tmpset, maxsetvec * sizeof(int)); if (setvec == 0 || tmpset == 0) overflo("out of space in first()"); } if (type(p) == EMPTYRE) { setvec[lp] = 0; return(0); } if (setvec[lp] != 1) { setvec[lp] = 1; setcnt++; } if (type(p) == CCL && (*(char *) right(p)) == '\0') return(0); /* empty CCL */ else return(1); case PLUS: if (first(left(p)) == 0) return(0); return(1); case STAR: case QUEST: first(left(p)); return(0); case CAT: if (first(left(p)) == 0 && first(right(p)) == 0) return(0); return(1); case OR: b = first(right(p)); if (first(left(p)) == 0 || b == 0) return(0); return(1); } FATAL("can't happen: unknown type %d in first", type(p)); /* can't happen */ return(-1); } void follow(Node *v) /* collects leaves that can follow v into setvec */ { Node *p; if (type(v) == FINAL) return; p = parent(v); switch (type(p)) { case STAR: case PLUS: first(v); follow(p); return; case OR: case QUEST: follow(p); return; case CAT: if (v == left(p)) { /* v is left child of p */ if (first(right(p)) == 0) { follow(p); return; } } else /* v is right child */ follow(p); return; } } int member(int c, const char *sarg) /* is c in s? */ { uschar *s = (uschar *) sarg; while (*s) if (c == *s++) return(1); return(0); } int match(fa *f, const char *p0) /* shortest match ? */ { int s, ns; uschar *p = (uschar *) p0; s = f->reset ? makeinit(f,0) : f->initstat; if (f->out[s]) return(1); do { /* assert(*p < NCHARS); */ if ((ns = f->gototab[s][*p]) != 0) s = ns; else s = cgoto(f, s, *p); if (f->out[s]) return(1); } while (*p++ != 0); return(0); } int pmatch(fa *f, const char *p0) /* longest match, for sub */ { int s, ns; uschar *p = (uschar *) p0; uschar *q; int i, k; /* s = f->reset ? makeinit(f,1) : f->initstat; */ if (f->reset) { f->initstat = s = makeinit(f,1); } else { s = f->initstat; } patbeg = (char *) p; patlen = -1; do { q = p; do { if (f->out[s]) /* final state */ patlen = q-p; /* assert(*q < NCHARS); */ if ((ns = f->gototab[s][*q]) != 0) s = ns; else s = cgoto(f, s, *q); if (s == 1) { /* no transition */ if (patlen >= 0) { patbeg = (char *) p; return(1); } else goto nextin; /* no match */ } } while (*q++ != 0); if (f->out[s]) patlen = q-p-1; /* don't count $ */ if (patlen >= 0) { patbeg = (char *) p; return(1); } nextin: s = 2; if (f->reset) { for (i = 2; i <= f->curstat; i++) xfree(f->posns[i]); k = *f->posns[0]; if ((f->posns[2] = (int *) calloc(1, (k+1)*sizeof(int))) == NULL) overflo("out of space in pmatch"); for (i = 0; i <= k; i++) (f->posns[2])[i] = (f->posns[0])[i]; f->initstat = f->curstat = 2; f->out[2] = f->out[0]; for (i = 0; i < NCHARS; i++) f->gototab[2][i] = 0; } } while (*p++ != 0); return (0); } int nematch(fa *f, const char *p0) /* non-empty match, for sub */ { int s, ns; uschar *p = (uschar *) p0; uschar *q; int i, k; /* s = f->reset ? makeinit(f,1) : f->initstat; */ if (f->reset) { f->initstat = s = makeinit(f,1); } else { s = f->initstat; } patlen = -1; while (*p) { q = p; do { if (f->out[s]) /* final state */ patlen = q-p; /* assert(*q < NCHARS); */ if ((ns = f->gototab[s][*q]) != 0) s = ns; else s = cgoto(f, s, *q); if (s == 1) { /* no transition */ if (patlen > 0) { patbeg = (char *) p; return(1); } else goto nnextin; /* no nonempty match */ } } while (*q++ != 0); if (f->out[s]) patlen = q-p-1; /* don't count $ */ if (patlen > 0 ) { patbeg = (char *) p; return(1); } nnextin: s = 2; if (f->reset) { for (i = 2; i <= f->curstat; i++) xfree(f->posns[i]); k = *f->posns[0]; if ((f->posns[2] = (int *) calloc(1, (k+1)*sizeof(int))) == NULL) overflo("out of state space"); for (i = 0; i <= k; i++) (f->posns[2])[i] = (f->posns[0])[i]; f->initstat = f->curstat = 2; f->out[2] = f->out[0]; for (i = 0; i < NCHARS; i++) f->gototab[2][i] = 0; } p++; } return (0); } Node *reparse(const char *p) /* parses regular expression pointed to by p */ { /* uses relex() to scan regular expression */ Node *np; dprintf( ("reparse <%s>\n", p) ); lastre = prestr = (uschar *) p; /* prestr points to string to be parsed */ rtok = relex(); /* GNU compatibility: an empty regexp matches anything */ if (rtok == '\0') { /* FATAL("empty regular expression"); previous */ return(op2(EMPTYRE, NIL, NIL)); } np = regexp(); if (rtok != '\0') FATAL("syntax error in regular expression %s at %s", lastre, prestr); return(np); } Node *regexp(void) /* top-level parse of reg expr */ { return (alt(concat(primary()))); } Node *primary(void) { Node *np; switch (rtok) { case CHAR: np = op2(CHAR, NIL, itonp(rlxval)); rtok = relex(); return (unary(np)); case ALL: rtok = relex(); return (unary(op2(ALL, NIL, NIL))); case EMPTYRE: rtok = relex(); return (unary(op2(ALL, NIL, NIL))); case DOT: rtok = relex(); return (unary(op2(DOT, NIL, NIL))); case CCL: np = op2(CCL, NIL, (Node*) cclenter((char *) rlxstr)); rtok = relex(); return (unary(np)); case NCCL: np = op2(NCCL, NIL, (Node *) cclenter((char *) rlxstr)); rtok = relex(); return (unary(np)); case '^': rtok = relex(); return (unary(op2(CHAR, NIL, itonp(HAT)))); case '$': rtok = relex(); return (unary(op2(CHAR, NIL, NIL))); case '(': rtok = relex(); if (rtok == ')') { /* special pleading for () */ rtok = relex(); return unary(op2(CCL, NIL, (Node *) tostring(""))); } np = regexp(); if (rtok == ')') { rtok = relex(); return (unary(np)); } else FATAL("syntax error in regular expression %s at %s", lastre, prestr); default: FATAL("illegal primary in regular expression %s at %s", lastre, prestr); } return 0; /*NOTREACHED*/ } Node *concat(Node *np) { switch (rtok) { case CHAR: case DOT: case ALL: case EMPTYRE: case CCL: case NCCL: case '$': case '(': return (concat(op2(CAT, np, primary()))); } return (np); } Node *alt(Node *np) { if (rtok == OR) { rtok = relex(); return (alt(op2(OR, np, concat(primary())))); } return (np); } Node *unary(Node *np) { switch (rtok) { case STAR: rtok = relex(); return (unary(op2(STAR, np, NIL))); case PLUS: rtok = relex(); return (unary(op2(PLUS, np, NIL))); case QUEST: rtok = relex(); return (unary(op2(QUEST, np, NIL))); default: return (np); } } /* * Character class definitions conformant to the POSIX locale as * defined in IEEE P1003.1 draft 7 of June 2001, assuming the source * and operating character sets are both ASCII (ISO646) or supersets * thereof. * * Note that to avoid overflowing the temporary buffer used in * relex(), the expanded character class (prior to range expansion) * must be less than twice the size of their full name. */ /* Because isblank doesn't show up in any of the header files on any * system i use, it's defined here. if some other locale has a richer * definition of "blank", define HAS_ISBLANK and provide your own * version. * the parentheses here are an attempt to find a path through the maze * of macro definition and/or function and/or version provided. thanks * to nelson beebe for the suggestion; let's see if it works everywhere. */ /* #define HAS_ISBLANK */ #ifndef HAS_ISBLANK int (xisblank)(int c) { return c==' ' || c=='\t'; } #endif struct charclass { const char *cc_name; int cc_namelen; int (*cc_func)(int); } charclasses[] = { { "alnum", 5, isalnum }, { "alpha", 5, isalpha }, #ifndef HAS_ISBLANK { "blank", 5, isspace }, /* was isblank */ #else { "blank", 5, isblank }, #endif { "cntrl", 5, iscntrl }, { "digit", 5, isdigit }, { "graph", 5, isgraph }, { "lower", 5, islower }, { "print", 5, isprint }, { "punct", 5, ispunct }, { "space", 5, isspace }, { "upper", 5, isupper }, { "xdigit", 6, isxdigit }, { NULL, 0, NULL }, }; int relex(void) /* lexical analyzer for reparse */ { int c, n; int cflag; static uschar *buf = 0; static int bufsz = 100; uschar *bp; struct charclass *cc; int i; switch (c = *prestr++) { case '|': return OR; case '*': return STAR; case '+': return PLUS; case '?': return QUEST; case '.': return DOT; case '\0': prestr--; return '\0'; case '^': case '$': case '(': case ')': return c; case '\\': rlxval = quoted(&prestr); return CHAR; default: rlxval = c; return CHAR; case '[': if (buf == 0 && (buf = (uschar *) malloc(bufsz)) == NULL) FATAL("out of space in reg expr %.10s..", lastre); bp = buf; if (*prestr == '^') { cflag = 1; prestr++; } else cflag = 0; n = 2 * strlen((const char *) prestr)+1; if (!adjbuf((char **) &buf, &bufsz, n, n, (char **) &bp, "relex1")) FATAL("out of space for reg expr %.10s...", lastre); for (; ; ) { if ((c = *prestr++) == '\\') { *bp++ = '\\'; if ((c = *prestr++) == '\0') FATAL("nonterminated character class %.20s...", lastre); *bp++ = c; /* } else if (c == '\n') { */ /* FATAL("newline in character class %.20s...", lastre); */ } else if (c == '[' && *prestr == ':') { /* POSIX char class names, Dag-Erling Smorgrav, des@ofug.org */ for (cc = charclasses; cc->cc_name; cc++) if (strncmp((const char *) prestr + 1, (const char *) cc->cc_name, cc->cc_namelen) == 0) break; if (cc->cc_name != NULL && prestr[1 + cc->cc_namelen] == ':' && prestr[2 + cc->cc_namelen] == ']') { prestr += cc->cc_namelen + 3; for (i = 0; i < NCHARS; i++) { if (!adjbuf((char **) &buf, &bufsz, bp-buf+1, 100, (char **) &bp, "relex2")) FATAL("out of space for reg expr %.10s...", lastre); if (cc->cc_func(i)) { *bp++ = i; n++; } } } else *bp++ = c; } else if (c == '\0') { FATAL("nonterminated character class %.20s", lastre); } else if (bp == buf) { /* 1st char is special */ *bp++ = c; } else if (c == ']') { *bp++ = 0; rlxstr = (uschar *) tostring((char *) buf); if (cflag == 0) return CCL; else return NCCL; } else *bp++ = c; } } } int cgoto(fa *f, int s, int c) { int i, j, k; int *p, *q; assert(c == HAT || c < NCHARS); while (f->accept >= maxsetvec) { /* guessing here! */ maxsetvec *= 4; setvec = (int *) realloc(setvec, maxsetvec * sizeof(int)); tmpset = (int *) realloc(tmpset, maxsetvec * sizeof(int)); if (setvec == 0 || tmpset == 0) overflo("out of space in cgoto()"); } for (i = 0; i <= f->accept; i++) setvec[i] = 0; setcnt = 0; /* compute positions of gototab[s,c] into setvec */ p = f->posns[s]; for (i = 1; i <= *p; i++) { if ((k = f->re[p[i]].ltype) != FINAL) { if ((k == CHAR && c == ptoi(f->re[p[i]].lval.np)) || (k == DOT && c != 0 && c != HAT) || (k == ALL && c != 0) || (k == EMPTYRE && c != 0) || (k == CCL && member(c, (char *) f->re[p[i]].lval.up)) || (k == NCCL && !member(c, (char *) f->re[p[i]].lval.up) && c != 0 && c != HAT)) { q = f->re[p[i]].lfollow; for (j = 1; j <= *q; j++) { if (q[j] >= maxsetvec) { maxsetvec *= 4; setvec = (int *) realloc(setvec, maxsetvec * sizeof(int)); tmpset = (int *) realloc(tmpset, maxsetvec * sizeof(int)); if (setvec == 0 || tmpset == 0) overflo("cgoto overflow"); } if (setvec[q[j]] == 0) { setcnt++; setvec[q[j]] = 1; } } } } } /* determine if setvec is a previous state */ tmpset[0] = setcnt; j = 1; for (i = f->accept; i >= 0; i--) if (setvec[i]) { tmpset[j++] = i; } /* tmpset == previous state? */ for (i = 1; i <= f->curstat; i++) { p = f->posns[i]; if ((k = tmpset[0]) != p[0]) goto different; for (j = 1; j <= k; j++) if (tmpset[j] != p[j]) goto different; /* setvec is state i */ f->gototab[s][c] = i; return i; different:; } /* add tmpset to current set of states */ if (f->curstat >= NSTATES-1) { f->curstat = 2; f->reset = 1; for (i = 2; i < NSTATES; i++) xfree(f->posns[i]); } else ++(f->curstat); for (i = 0; i < NCHARS; i++) f->gototab[f->curstat][i] = 0; xfree(f->posns[f->curstat]); if ((p = (int *) calloc(1, (setcnt+1)*sizeof(int))) == NULL) overflo("out of space in cgoto"); f->posns[f->curstat] = p; f->gototab[s][c] = f->curstat; for (i = 0; i <= setcnt; i++) p[i] = tmpset[i]; if (setvec[f->accept]) f->out[f->curstat] = 1; else f->out[f->curstat] = 0; return f->curstat; } void freefa(fa *f) /* free a finite automaton */ { int i; if (f == NULL) return; for (i = 0; i <= f->curstat; i++) xfree(f->posns[i]); for (i = 0; i <= f->accept; i++) { xfree(f->re[i].lfollow); if (f->re[i].ltype == CCL || f->re[i].ltype == NCCL) xfree((f->re[i].lval.np)); } xfree(f->restr); xfree(f); } bioawk-1.0/kseq.h000066400000000000000000000211531220715177100137470ustar00rootroot00000000000000/* The MIT License Copyright (c) 2008, 2009, 2011 Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Last Modified: 05MAR2012 */ #ifndef AC_KSEQ_H #define AC_KSEQ_H #include #include #include #define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r #define KS_SEP_TAB 1 // isspace() && !' ' #define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows) #define KS_SEP_MAX 2 #define __KS_TYPE(type_t) \ typedef struct __kstream_t { \ unsigned char *buf; \ int begin, end, is_eof; \ type_t f; \ } kstream_t; #define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end) #define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0) #define __KS_BASIC(type_t, __bufsize) \ static inline kstream_t *ks_init(type_t f) \ { \ kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \ ks->f = f; \ ks->buf = (unsigned char*)malloc(__bufsize); \ return ks; \ } \ static inline void ks_destroy(kstream_t *ks) \ { \ if (ks) { \ free(ks->buf); \ free(ks); \ } \ } #define __KS_GETC(__read, __bufsize) \ static inline int ks_getc(kstream_t *ks) \ { \ if (ks->is_eof && ks->begin >= ks->end) return -1; \ if (ks->begin >= ks->end) { \ ks->begin = 0; \ ks->end = __read(ks->f, ks->buf, __bufsize); \ if (ks->end < __bufsize) ks->is_eof = 1; \ if (ks->end == 0) return -1; \ } \ return (int)ks->buf[ks->begin++]; \ } #ifndef KSTRING_T #define KSTRING_T kstring_t typedef struct __kstring_t { size_t l, m; char *s; } kstring_t; #endif #ifndef kroundup32 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif #define __KS_GETUNTIL(__read, __bufsize) \ static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \ { \ if (dret) *dret = 0; \ str->l = append? str->l : 0; \ if (ks->begin >= ks->end && ks->is_eof) return -1; \ for (;;) { \ int i; \ if (ks->begin >= ks->end) { \ if (!ks->is_eof) { \ ks->begin = 0; \ ks->end = __read(ks->f, ks->buf, __bufsize); \ if (ks->end < __bufsize) ks->is_eof = 1; \ if (ks->end == 0) break; \ } else break; \ } \ if (delimiter == KS_SEP_LINE) { \ for (i = ks->begin; i < ks->end; ++i) \ if (ks->buf[i] == '\n') break; \ } else if (delimiter > KS_SEP_MAX) { \ for (i = ks->begin; i < ks->end; ++i) \ if (ks->buf[i] == delimiter) break; \ } else if (delimiter == KS_SEP_SPACE) { \ for (i = ks->begin; i < ks->end; ++i) \ if (isspace(ks->buf[i])) break; \ } else if (delimiter == KS_SEP_TAB) { \ for (i = ks->begin; i < ks->end; ++i) \ if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \ } else i = 0; /* never come to here! */ \ if (str->m - str->l < (size_t)(i - ks->begin + 1)) { \ str->m = str->l + (i - ks->begin) + 1; \ kroundup32(str->m); \ str->s = (char*)realloc(str->s, str->m); \ } \ memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \ str->l = str->l + (i - ks->begin); \ ks->begin = i + 1; \ if (i < ks->end) { \ if (dret) *dret = ks->buf[i]; \ break; \ } \ } \ if (str->s == 0) { \ str->m = 1; \ str->s = (char*)calloc(1, 1); \ } else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l-1] == '\r') --str->l; \ str->s[str->l] = '\0'; \ return str->l; \ } \ static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \ { return ks_getuntil2(ks, delimiter, str, dret, 0); } #define KSTREAM_INIT(type_t, __read, __bufsize) \ __KS_TYPE(type_t) \ __KS_BASIC(type_t, __bufsize) \ __KS_GETC(__read, __bufsize) \ __KS_GETUNTIL(__read, __bufsize) #define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0) #define __KSEQ_BASIC(SCOPE, type_t) \ SCOPE kseq_t *kseq_init(type_t fd) \ { \ kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \ s->f = ks_init(fd); \ return s; \ } \ SCOPE void kseq_destroy(kseq_t *ks) \ { \ if (!ks) return; \ free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \ ks_destroy(ks->f); \ free(ks); \ } /* Return value: >=0 length of the sequence (normal) -1 end-of-file -2 truncated quality string */ #define __KSEQ_READ(SCOPE) \ SCOPE int kseq_read(kseq_t *seq) \ { \ int c; \ kstream_t *ks = seq->f; \ if (seq->last_char == 0) { /* then jump to the next header line */ \ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \ if (c == -1) return -1; /* end of file */ \ seq->last_char = c; \ } /* else: the first header char has been read in the previous call */ \ seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \ if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \ if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \ if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \ seq->seq.m = 256; \ seq->seq.s = (char*)malloc(seq->seq.m); \ } \ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \ if (c == '\n') continue; /* skip empty lines */ \ seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \ ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \ } \ if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \ if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \ seq->seq.m = seq->seq.l + 2; \ kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \ seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \ } \ seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \ if (c != '+') return seq->seq.l; /* FASTA */ \ if (seq->qual.m < seq->seq.m) { /* allocate memory for qual in case insufficient */ \ seq->qual.m = seq->seq.m; \ seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \ } \ while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \ if (c == -1) return -2; /* error: no quality string */ \ while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \ seq->last_char = 0; /* we have not come to the next header line */ \ if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \ return seq->seq.l; \ } #define __KSEQ_TYPE(type_t) \ typedef struct { \ kstring_t name, comment, seq, qual; \ int last_char; \ kstream_t *f; \ } kseq_t; #define KSEQ_INIT2(SCOPE, type_t, __read) \ KSTREAM_INIT(type_t, __read, 16384) \ __KSEQ_TYPE(type_t) \ __KSEQ_BASIC(SCOPE, type_t) \ __KSEQ_READ(SCOPE) #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) #define KSEQ_DECLARE(type_t) \ __KS_TYPE(type_t) \ __KSEQ_TYPE(type_t) \ extern kseq_t *kseq_init(type_t fd); \ void kseq_destroy(kseq_t *ks); \ int kseq_read(kseq_t *seq); #endif bioawk-1.0/lex.c000066400000000000000000000321331220715177100135670ustar00rootroot00000000000000/**************************************************************** Copyright (C) Lucent Technologies 1997 All Rights Reserved Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that the copyright notice and this permission notice and warranty disclaimer appear in supporting documentation, and that the name Lucent Technologies or any of its entities not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ****************************************************************/ #include #include #include #include #include "awk.h" #include "ytab.h" extern YYSTYPE yylval; extern int infunc; int lineno = 1; int bracecnt = 0; int brackcnt = 0; int parencnt = 0; typedef struct Keyword { const char *word; int sub; int type; } Keyword; Keyword keywords[] ={ /* keep sorted: binary searched */ { "BEGIN", XBEGIN, XBEGIN }, { "END", XEND, XEND }, { "NF", VARNF, VARNF }, { "and", BIO_FAND, BLTIN }, { "atan2", FATAN, BLTIN }, { "break", BREAK, BREAK }, { "close", CLOSE, CLOSE }, { "continue", CONTINUE, CONTINUE }, { "cos", FCOS, BLTIN }, { "delete", DELETE, DELETE }, { "do", DO, DO }, { "else", ELSE, ELSE }, { "exit", EXIT, EXIT }, { "exp", FEXP, BLTIN }, { "fflush", FFLUSH, BLTIN }, { "for", FOR, FOR }, { "func", FUNC, FUNC }, { "function", FUNC, FUNC }, { "gc", BIO_FGC, BLTIN }, { "getline", GETLINE, GETLINE }, { "gsub", GSUB, GSUB }, { "if", IF, IF }, { "in", IN, IN }, { "index", INDEX, INDEX }, { "int", FINT, BLTIN }, { "length", FLENGTH, BLTIN }, { "log", FLOG, BLTIN }, { "match", MATCHFCN, MATCHFCN }, { "meanqual", BIO_FMEANQUAL, BLTIN }, { "next", NEXT, NEXT }, { "nextfile", NEXTFILE, NEXTFILE }, { "or", BIO_FOR, BLTIN }, { "print", PRINT, PRINT }, { "printf", PRINTF, PRINTF }, { "qualcount", BIO_FQUALCOUNT, BLTIN }, { "rand", FRAND, BLTIN }, { "return", RETURN, RETURN }, { "revcomp",BIO_FREVCOMP, BLTIN }, { "reverse",BIO_FREVERSE, BLTIN }, { "sin", FSIN, BLTIN }, { "split", SPLIT, SPLIT }, { "sprintf", SPRINTF, SPRINTF }, { "sqrt", FSQRT, BLTIN }, { "srand", FSRAND, BLTIN }, { "sub", SUB, SUB }, { "substr", SUBSTR, SUBSTR }, { "system", FSYSTEM, BLTIN }, { "tolower", FTOLOWER, BLTIN }, { "toupper", FTOUPPER, BLTIN }, { "trimq", BIO_FTRIMQ, BLTIN }, { "while", WHILE, WHILE }, { "xor", BIO_FXOR, BLTIN } }; #define RET(x) { if(dbg)printf("lex %s\n", tokname(x)); return(x); } int peek(void) { int c = input(); unput(c); return c; } int gettok(char **pbuf, int *psz) /* get next input token */ { int c, retc; char *buf = *pbuf; int sz = *psz; char *bp = buf; c = input(); if (c == 0) return 0; buf[0] = c; buf[1] = 0; if (!isalnum(c) && c != '.' && c != '_') return c; *bp++ = c; if (isalpha(c) || c == '_') { /* it's a varname */ for ( ; (c = input()) != 0; ) { if (bp-buf >= sz) if (!adjbuf(&buf, &sz, bp-buf+2, 100, &bp, "gettok")) FATAL( "out of space for name %.10s...", buf ); if (isalnum(c) || c == '_') *bp++ = c; else { *bp = 0; unput(c); break; } } *bp = 0; retc = 'a'; /* alphanumeric */ } else { /* maybe it's a number, but could be . */ char *rem; /* read input until can't be a number */ for ( ; (c = input()) != 0; ) { if (bp-buf >= sz) if (!adjbuf(&buf, &sz, bp-buf+2, 100, &bp, "gettok")) FATAL( "out of space for number %.10s...", buf ); if (isdigit(c) || c == 'e' || c == 'E' || c == '.' || c == '+' || c == '-') *bp++ = c; else { unput(c); break; } } *bp = 0; strtod(buf, &rem); /* parse the number */ if (rem == buf) { /* it wasn't a valid number at all */ buf[1] = 0; /* return one character as token */ retc = buf[0]; /* character is its own type */ unputstr(rem+1); /* put rest back for later */ } else { /* some prefix was a number */ unputstr(rem); /* put rest back for later */ rem[0] = 0; /* truncate buf after number part */ retc = '0'; /* type is number */ } } *pbuf = buf; *psz = sz; return retc; } int word(char *); int string(void); int regexpr(void); int sc = 0; /* 1 => return a } right now */ int reg = 0; /* 1 => return a REGEXPR now */ int yylex(void) { int c; static char *buf = 0; static int bufsize = 5; /* BUG: setting this small causes core dump! */ if (buf == 0 && (buf = (char *) malloc(bufsize)) == NULL) FATAL( "out of space in yylex" ); if (sc) { sc = 0; RET('}'); } if (reg) { reg = 0; return regexpr(); } for (;;) { c = gettok(&buf, &bufsize); if (c == 0) return 0; if (isalpha(c) || c == '_') return word(buf); if (isdigit(c)) { yylval.cp = setsymtab(buf, tostring(buf), atof(buf), CON|NUM, symtab); /* should this also have STR set? */ RET(NUMBER); } yylval.i = c; switch (c) { case '\n': /* {EOL} */ RET(NL); case '\r': /* assume \n is coming */ case ' ': /* {WS}+ */ case '\t': break; case '#': /* #.* strip comments */ while ((c = input()) != '\n' && c != 0) ; unput(c); break; case ';': RET(';'); case '\\': if (peek() == '\n') { input(); } else if (peek() == '\r') { input(); input(); /* \n */ lineno++; } else { RET(c); } break; case '&': if (peek() == '&') { input(); RET(AND); } else RET('&'); case '|': if (peek() == '|') { input(); RET(BOR); } else RET('|'); case '!': if (peek() == '=') { input(); yylval.i = NE; RET(NE); } else if (peek() == '~') { input(); yylval.i = NOTMATCH; RET(MATCHOP); } else RET(NOT); case '~': yylval.i = MATCH; RET(MATCHOP); case '<': if (peek() == '=') { input(); yylval.i = LE; RET(LE); } else { yylval.i = LT; RET(LT); } case '=': if (peek() == '=') { input(); yylval.i = EQ; RET(EQ); } else { yylval.i = ASSIGN; RET(ASGNOP); } case '>': if (peek() == '=') { input(); yylval.i = GE; RET(GE); } else if (peek() == '>') { input(); yylval.i = APPEND; RET(APPEND); } else { yylval.i = GT; RET(GT); } case '+': if (peek() == '+') { input(); yylval.i = INCR; RET(INCR); } else if (peek() == '=') { input(); yylval.i = ADDEQ; RET(ASGNOP); } else RET('+'); case '-': if (peek() == '-') { input(); yylval.i = DECR; RET(DECR); } else if (peek() == '=') { input(); yylval.i = SUBEQ; RET(ASGNOP); } else RET('-'); case '*': if (peek() == '=') { /* *= */ input(); yylval.i = MULTEQ; RET(ASGNOP); } else if (peek() == '*') { /* ** or **= */ input(); /* eat 2nd * */ if (peek() == '=') { input(); yylval.i = POWEQ; RET(ASGNOP); } else { RET(POWER); } } else RET('*'); case '/': RET('/'); case '%': if (peek() == '=') { input(); yylval.i = MODEQ; RET(ASGNOP); } else RET('%'); case '^': if (peek() == '=') { input(); yylval.i = POWEQ; RET(ASGNOP); } else RET(POWER); case '$': /* BUG: awkward, if not wrong */ c = gettok(&buf, &bufsize); if (isalpha(c)) { if (strcmp(buf, "NF") == 0) { /* very special */ unputstr("(NF)"); RET(INDIRECT); } c = peek(); if (c == '(' || c == '[' || (infunc && isarg(buf) >= 0)) { unputstr(buf); RET(INDIRECT); } yylval.cp = setsymtab(buf, "", 0.0, STR|NUM, symtab); RET(IVAR); } else if (c == 0) { /* */ SYNTAX( "unexpected end of input after $" ); RET(';'); } else { unputstr(buf); RET(INDIRECT); } case '}': if (--bracecnt < 0) SYNTAX( "extra }" ); sc = 1; RET(';'); case ']': if (--brackcnt < 0) SYNTAX( "extra ]" ); RET(']'); case ')': if (--parencnt < 0) SYNTAX( "extra )" ); RET(')'); case '{': bracecnt++; RET('{'); case '[': brackcnt++; RET('['); case '(': parencnt++; RET('('); case '"': return string(); /* BUG: should be like tran.c ? */ default: RET(c); } } } int string(void) { int c, n; char *s, *bp; static char *buf = 0; static int bufsz = 500; if (buf == 0 && (buf = (char *) malloc(bufsz)) == NULL) FATAL("out of space for strings"); for (bp = buf; (c = input()) != '"'; ) { if (!adjbuf(&buf, &bufsz, bp-buf+2, 500, &bp, "string")) FATAL("out of space for string %.10s...", buf); switch (c) { case '\n': case '\r': case 0: SYNTAX( "non-terminated string %.10s...", buf ); lineno++; if (c == 0) /* hopeless */ FATAL( "giving up" ); break; case '\\': c = input(); switch (c) { case '"': *bp++ = '"'; break; case 'n': *bp++ = '\n'; break; case 't': *bp++ = '\t'; break; case 'f': *bp++ = '\f'; break; case 'r': *bp++ = '\r'; break; case 'b': *bp++ = '\b'; break; case 'v': *bp++ = '\v'; break; case 'a': *bp++ = '\007'; break; case '\\': *bp++ = '\\'; break; case '0': case '1': case '2': /* octal: \d \dd \ddd */ case '3': case '4': case '5': case '6': case '7': n = c - '0'; if ((c = peek()) >= '0' && c < '8') { n = 8 * n + input() - '0'; if ((c = peek()) >= '0' && c < '8') n = 8 * n + input() - '0'; } *bp++ = n; break; case 'x': /* hex \x0-9a-fA-F + */ { char xbuf[100], *px; for (px = xbuf; (c = input()) != 0 && px-xbuf < 100-2; ) { if (isdigit(c) || (c >= 'a' && c <= 'f') || (c >= 'A' && c <= 'F')) *px++ = c; else break; } *px = 0; unput(c); sscanf(xbuf, "%x", (unsigned int *) &n); *bp++ = n; break; } default: *bp++ = c; break; } break; default: *bp++ = c; break; } } *bp = 0; s = tostring(buf); *bp++ = ' '; *bp++ = 0; yylval.cp = setsymtab(buf, s, 0.0, CON|STR|DONTFREE, symtab); RET(STRING); } int binsearch(char *w, Keyword *kp, int n) { int cond, low, mid, high; low = 0; high = n - 1; while (low <= high) { mid = (low + high) / 2; if ((cond = strcmp(w, kp[mid].word)) < 0) high = mid - 1; else if (cond > 0) low = mid + 1; else return mid; } return -1; } int word(char *w) { Keyword *kp; int c, n; n = binsearch(w, keywords, sizeof(keywords)/sizeof(keywords[0])); /* BUG: this ought to be inside the if; in theory could fault (daniel barrett) */ kp = keywords + n; if (n != -1) { /* found in table */ yylval.i = kp->sub; switch (kp->type) { /* special handling */ case BLTIN: if (kp->sub == FSYSTEM && safe) SYNTAX( "system is unsafe" ); RET(kp->type); case FUNC: if (infunc) SYNTAX( "illegal nested function" ); RET(kp->type); case RETURN: if (!infunc) SYNTAX( "return not in function" ); RET(kp->type); case VARNF: yylval.cp = setsymtab("NF", "", 0.0, NUM, symtab); RET(VARNF); default: RET(kp->type); } } c = peek(); /* look for '(' */ if (c != '(' && infunc && (n=isarg(w)) >= 0) { yylval.i = n; RET(ARG); } else { yylval.cp = setsymtab(w, "", 0.0, STR|NUM|DONTFREE, symtab); if (c == '(') { RET(CALL); } else { RET(VAR); } } } void startreg(void) /* next call to yylex will return a regular expression */ { reg = 1; } int regexpr(void) { int c; static char *buf = 0; static int bufsz = 500; char *bp; if (buf == 0 && (buf = (char *) malloc(bufsz)) == NULL) FATAL("out of space for rex expr"); bp = buf; for ( ; (c = input()) != '/' && c != 0; ) { if (!adjbuf(&buf, &bufsz, bp-buf+3, 500, &bp, "regexpr")) FATAL("out of space for reg expr %.10s...", buf); if (c == '\n') { SYNTAX( "newline in regular expression %.10s...", buf ); unput('\n'); break; } else if (c == '\\') { *bp++ = '\\'; *bp++ = input(); } else { *bp++ = c; } } *bp = 0; if (c == 0) SYNTAX("non-terminated regular expression %.10s...", buf); yylval.s = tostring(buf); unput('/'); RET(REGEXPR); } /* low-level lexical stuff, sort of inherited from lex */ char ebuf[300]; char *ep = ebuf; char yysbuf[100]; /* pushback buffer */ char *yysptr = yysbuf; FILE *yyin = 0; int input(void) /* get next lexical input character */ { int c; extern char *lexprog; if (yysptr > yysbuf) c = (uschar)*--yysptr; else if (lexprog != NULL) { /* awk '...' */ if ((c = (uschar)*lexprog) != 0) lexprog++; } else /* awk -f ... */ c = pgetc(); if (c == '\n') lineno++; else if (c == EOF) c = 0; if (ep >= ebuf + sizeof ebuf) ep = ebuf; return *ep++ = c; } void unput(int c) /* put lexical character back on input */ { if (c == '\n') lineno--; if (yysptr >= yysbuf + sizeof(yysbuf)) FATAL("pushed back too much: %.20s...", yysbuf); *yysptr++ = c; if (--ep < ebuf) ep = ebuf + sizeof(ebuf) - 1; } void unputstr(const char *s) /* put a string back on input */ { int i; for (i = strlen(s)-1; i >= 0; i--) unput(s[i]); } bioawk-1.0/lib.c000066400000000000000000000420041220715177100135430ustar00rootroot00000000000000/**************************************************************** Copyright (C) Lucent Technologies 1997 All Rights Reserved Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that the copyright notice and this permission notice and warranty disclaimer appear in supporting documentation, and that the name Lucent Technologies or any of its entities not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ****************************************************************/ #define DEBUG #include #include #include #include #include #include #include "awk.h" #include "ytab.h" FILE *infile = NULL; char *file = ""; char *record; int recsize = RECSIZE; char *fields; int fieldssize = RECSIZE; Cell **fldtab; /* pointers to Cells */ char inputFS[100] = " "; #define MAXFLD 2 int nfields = MAXFLD; /* last allocated slot for $i */ int donefld; /* 1 = implies rec broken into fields */ int donerec; /* 1 = record is valid (no flds have changed) */ int lastfld = 0; /* last used field */ int argno = 1; /* current input argument number */ extern Awkfloat *ARGC; static Cell dollar0 = { OCELL, CFLD, NULL, "", 0.0, REC|STR|DONTFREE }; static Cell dollar1 = { OCELL, CFLD, NULL, "", 0.0, FLD|STR|DONTFREE }; void recinit(unsigned int n) { if ( (record = (char *) malloc(n)) == NULL || (fields = (char *) malloc(n+1)) == NULL || (fldtab = (Cell **) malloc((nfields+1) * sizeof(Cell *))) == NULL || (fldtab[0] = (Cell *) malloc(sizeof(Cell))) == NULL ) FATAL("out of space for $0 and fields"); *fldtab[0] = dollar0; fldtab[0]->sval = record; fldtab[0]->nval = tostring("0"); makefields(1, nfields); } void makefields(int n1, int n2) /* create $n1..$n2 inclusive */ { char temp[50]; int i; for (i = n1; i <= n2; i++) { fldtab[i] = (Cell *) malloc(sizeof (struct Cell)); if (fldtab[i] == NULL) FATAL("out of space in makefields %d", i); *fldtab[i] = dollar1; sprintf(temp, "%d", i); fldtab[i]->nval = tostring(temp); } } void initgetrec(void) { int i; char *p; for (i = 1; i < *ARGC; i++) { p = getargv(i); /* find 1st real filename */ if (p == NULL || *p == '\0') { /* deleted or zapped */ argno++; continue; } if (!isclvar(p)) { setsval(lookup("FILENAME", symtab), p); return; } setclvar(p); /* a commandline assignment before filename */ argno++; } infile = stdin; /* no filenames, so use stdin */ } static int firsttime = 1; int getrec(char **pbuf, int *pbufsize, int isrecord) /* get next input record */ { /* note: cares whether buf == record */ int c; char *buf = *pbuf; uschar saveb0; int bufsize = *pbufsize, savebufsize = bufsize; if (bio_fmt != BIO_NULL) return bio_getrec(pbuf, pbufsize, isrecord); if (firsttime) { firsttime = 0; initgetrec(); } dprintf( ("RS=<%s>, FS=<%s>, ARGC=%g, FILENAME=%s\n", *RS, *FS, *ARGC, *FILENAME) ); if (isrecord) { donefld = 0; donerec = 1; } saveb0 = buf[0]; buf[0] = 0; while (argno < *ARGC || infile == stdin) { dprintf( ("argno=%d, file=|%s|\n", argno, file) ); if (infile == NULL) { /* have to open a new file */ file = getargv(argno); if (file == NULL || *file == '\0') { /* deleted or zapped */ argno++; continue; } if (isclvar(file)) { /* a var=value arg */ setclvar(file); argno++; continue; } *FILENAME = file; dprintf( ("opening file %s\n", file) ); if (*file == '-' && *(file+1) == '\0') infile = stdin; else if ((infile = fopen(file, "r")) == NULL) FATAL("can't open file %s", file); setfval(fnrloc, 0.0); } c = readrec(&buf, &bufsize, infile); if (c != 0 || buf[0] != '\0') { /* normal record */ if (isrecord) { if (freeable(fldtab[0])) xfree(fldtab[0]->sval); fldtab[0]->sval = buf; /* buf == record */ fldtab[0]->tval = REC | STR | DONTFREE; if (is_number(fldtab[0]->sval)) { fldtab[0]->fval = atof(fldtab[0]->sval); fldtab[0]->tval |= NUM; } } setfval(nrloc, nrloc->fval+1); setfval(fnrloc, fnrloc->fval+1); *pbuf = buf; *pbufsize = bufsize; return 1; } /* EOF arrived on this file; set up next */ if (infile != stdin) fclose(infile); infile = NULL; argno++; } buf[0] = saveb0; *pbuf = buf; *pbufsize = savebufsize; return 0; /* true end of file */ } void nextfile(void) { if (infile != NULL && infile != stdin) fclose(infile); infile = NULL; argno++; } int readrec(char **pbuf, int *pbufsize, FILE *inf) /* read one record into buf */ { int sep, c; char *rr, *buf = *pbuf; int bufsize = *pbufsize; if (strlen(*FS) >= sizeof(inputFS)) FATAL("field separator %.10s... is too long", *FS); /*fflush(stdout); avoids some buffering problem but makes it 25% slower*/ strcpy(inputFS, *FS); /* for subsequent field splitting */ if ((sep = **RS) == 0) { sep = '\n'; while ((c=getc(inf)) == '\n' && c != EOF) /* skip leading \n's */ ; if (c != EOF) ungetc(c, inf); } for (rr = buf; ; ) { for (; (c=getc(inf)) != sep && c != EOF; ) { if (rr-buf+1 > bufsize) if (!adjbuf(&buf, &bufsize, 1+rr-buf, recsize, &rr, "readrec 1")) FATAL("input record `%.30s...' too long", buf); *rr++ = c; } if (**RS == sep || c == EOF) break; if ((c = getc(inf)) == '\n' || c == EOF) /* 2 in a row */ break; if (!adjbuf(&buf, &bufsize, 2+rr-buf, recsize, &rr, "readrec 2")) FATAL("input record `%.30s...' too long", buf); *rr++ = '\n'; *rr++ = c; } if (!adjbuf(&buf, &bufsize, 1+rr-buf, recsize, &rr, "readrec 3")) FATAL("input record `%.30s...' too long", buf); *rr = 0; dprintf( ("readrec saw <%s>, returns %d\n", buf, c == EOF && rr == buf ? 0 : 1) ); *pbuf = buf; *pbufsize = bufsize; return c == EOF && rr == buf ? 0 : 1; } char *getargv(int n) /* get ARGV[n] */ { Cell *x; char *s, temp[50]; extern Array *ARGVtab; sprintf(temp, "%d", n); if (lookup(temp, ARGVtab) == NULL) return NULL; x = setsymtab(temp, "", 0.0, STR, ARGVtab); s = getsval(x); dprintf( ("getargv(%d) returns |%s|\n", n, s) ); return s; } void setclvar(char *s) /* set var=value from s */ { char *p; Cell *q; for (p=s; *p != '='; p++) ; *p++ = 0; p = qstring(p, '\0'); q = setsymtab(s, p, 0.0, STR, symtab); setsval(q, p); if (is_number(q->sval)) { q->fval = atof(q->sval); q->tval |= NUM; } dprintf( ("command line set %s to |%s|\n", s, p) ); } void fldbld(void) /* create fields from current record */ { /* this relies on having fields[] the same length as $0 */ /* the fields are all stored in this one array with \0's */ /* possibly with a final trailing \0 not associated with any field */ char *r, *fr, sep; Cell *p; int i, j, n; if (donefld) return; if (!isstr(fldtab[0])) getsval(fldtab[0]); r = fldtab[0]->sval; n = strlen(r); if (n > fieldssize) { xfree(fields); if ((fields = (char *) malloc(n+2)) == NULL) /* possibly 2 final \0s */ FATAL("out of space for fields in fldbld %d", n); fieldssize = n; } fr = fields; i = 0; /* number of fields accumulated here */ strcpy(inputFS, *FS); if (strlen(inputFS) > 1) { /* it's a regular expression */ i = refldbld(r, inputFS); } else if ((sep = *inputFS) == ' ') { /* default whitespace */ for (i = 0; ; ) { while (*r == ' ' || *r == '\t' || *r == '\n') r++; if (*r == 0) break; i++; if (i > nfields) growfldtab(i); if (freeable(fldtab[i])) xfree(fldtab[i]->sval); fldtab[i]->sval = fr; fldtab[i]->tval = FLD | STR | DONTFREE; do *fr++ = *r++; while (*r != ' ' && *r != '\t' && *r != '\n' && *r != '\0'); *fr++ = 0; } *fr = 0; } else if ((sep = *inputFS) == 0) { /* new: FS="" => 1 char/field */ for (i = 0; *r != 0; r++) { char buf[2]; i++; if (i > nfields) growfldtab(i); if (freeable(fldtab[i])) xfree(fldtab[i]->sval); buf[0] = *r; buf[1] = 0; fldtab[i]->sval = tostring(buf); fldtab[i]->tval = FLD | STR; } *fr = 0; } else if (*r != 0) { /* if 0, it's a null field */ /* subtlecase : if length(FS) == 1 && length(RS > 0) * \n is NOT a field separator (cf awk book 61,84). * this variable is tested in the inner while loop. */ int rtest = '\n'; /* normal case */ if (strlen(*RS) > 0) rtest = '\0'; for (;;) { i++; if (i > nfields) growfldtab(i); if (freeable(fldtab[i])) xfree(fldtab[i]->sval); fldtab[i]->sval = fr; fldtab[i]->tval = FLD | STR | DONTFREE; while (*r != sep && *r != rtest && *r != '\0') /* \n is always a separator */ *fr++ = *r++; *fr++ = 0; if (*r++ == 0) break; } *fr = 0; } if (i > nfields) FATAL("record `%.30s...' has too many fields; can't happen", r); cleanfld(i+1, lastfld); /* clean out junk from previous record */ lastfld = i; donefld = 1; for (j = 1; j <= lastfld; j++) { p = fldtab[j]; if(is_number(p->sval)) { p->fval = atof(p->sval); p->tval |= NUM; } } setfval(nfloc, (Awkfloat) lastfld); if (dbg) { for (j = 0; j <= lastfld; j++) { p = fldtab[j]; printf("field %d (%s): |%s|\n", j, p->nval, p->sval); } } } void cleanfld(int n1, int n2) /* clean out fields n1 .. n2 inclusive */ { /* nvals remain intact */ Cell *p; int i; for (i = n1; i <= n2; i++) { p = fldtab[i]; if (freeable(p)) xfree(p->sval); p->sval = ""; p->tval = FLD | STR | DONTFREE; } } void newfld(int n) /* add field n after end of existing lastfld */ { if (n > nfields) growfldtab(n); cleanfld(lastfld+1, n); lastfld = n; setfval(nfloc, (Awkfloat) n); } Cell *fieldadr(int n) /* get nth field */ { if (n < 0) FATAL("trying to access out of range field %d", n); if (n > nfields) /* fields after NF are empty */ growfldtab(n); /* but does not increase NF */ return(fldtab[n]); } void growfldtab(int n) /* make new fields up to at least $n */ { int nf = 2 * nfields; size_t s; if (n > nf) nf = n; s = (nf+1) * (sizeof (struct Cell *)); /* freebsd: how much do we need? */ if (s / sizeof(struct Cell *) - 1 == nf) /* didn't overflow */ fldtab = (Cell **) realloc(fldtab, s); else /* overflow sizeof int */ xfree(fldtab); /* make it null */ if (fldtab == NULL) FATAL("out of space creating %d fields", nf); makefields(nfields+1, nf); nfields = nf; } int refldbld(const char *rec, const char *fs) /* build fields from reg expr in FS */ { /* this relies on having fields[] the same length as $0 */ /* the fields are all stored in this one array with \0's */ char *fr; int i, tempstat, n; fa *pfa; n = strlen(rec); if (n > fieldssize) { xfree(fields); if ((fields = (char *) malloc(n+1)) == NULL) FATAL("out of space for fields in refldbld %d", n); fieldssize = n; } fr = fields; *fr = '\0'; if (*rec == '\0') return 0; pfa = makedfa(fs, 1); dprintf( ("into refldbld, rec = <%s>, pat = <%s>\n", rec, fs) ); tempstat = pfa->initstat; for (i = 1; ; i++) { if (i > nfields) growfldtab(i); if (freeable(fldtab[i])) xfree(fldtab[i]->sval); fldtab[i]->tval = FLD | STR | DONTFREE; fldtab[i]->sval = fr; dprintf( ("refldbld: i=%d\n", i) ); if (nematch(pfa, rec)) { pfa->initstat = 2; /* horrible coupling to b.c */ dprintf( ("match %s (%d chars)\n", patbeg, patlen) ); strncpy(fr, rec, patbeg-rec); fr += patbeg - rec + 1; *(fr-1) = '\0'; rec = patbeg + patlen; } else { dprintf( ("no match %s\n", rec) ); strcpy(fr, rec); pfa->initstat = tempstat; break; } } return i; } void recbld(void) /* create $0 from $1..$NF if necessary */ { int i; char *r, *p; if (donerec == 1) return; r = record; for (i = 1; i <= *NF; i++) { p = getsval(fldtab[i]); if (!adjbuf(&record, &recsize, 1+strlen(p)+r-record, recsize, &r, "recbld 1")) FATAL("created $0 `%.30s...' too long", record); while ((*r = *p++) != 0) r++; if (i < *NF) { if (!adjbuf(&record, &recsize, 2+strlen(*OFS)+r-record, recsize, &r, "recbld 2")) FATAL("created $0 `%.30s...' too long", record); for (p = *OFS; (*r = *p++) != 0; ) r++; } } if (!adjbuf(&record, &recsize, 2+r-record, recsize, &r, "recbld 3")) FATAL("built giant record `%.30s...'", record); *r = '\0'; dprintf( ("in recbld inputFS=%s, fldtab[0]=%p\n", inputFS, (void*)fldtab[0]) ); if (freeable(fldtab[0])) xfree(fldtab[0]->sval); fldtab[0]->tval = REC | STR | DONTFREE; fldtab[0]->sval = record; dprintf( ("in recbld inputFS=%s, fldtab[0]=%p\n", inputFS, (void*)fldtab[0]) ); dprintf( ("recbld = |%s|\n", record) ); donerec = 1; } int errorflag = 0; void yyerror(const char *s) { SYNTAX("%s", s); } void SYNTAX(const char *fmt, ...) { extern char *cmdname, *curfname; static int been_here = 0; va_list varg; if (been_here++ > 2) return; fprintf(stderr, "%s: ", cmdname); va_start(varg, fmt); vfprintf(stderr, fmt, varg); va_end(varg); fprintf(stderr, " at source line %d", lineno); if (curfname != NULL) fprintf(stderr, " in function %s", curfname); if (compile_time == 1 && cursource() != NULL) fprintf(stderr, " source file %s", cursource()); fprintf(stderr, "\n"); errorflag = 2; eprint(); } void fpecatch(int n) { FATAL("floating point exception %d", n); } extern int bracecnt, brackcnt, parencnt; void bracecheck(void) { int c; static int beenhere = 0; if (beenhere++) return; while ((c = input()) != EOF && c != '\0') bclass(c); bcheck2(bracecnt, '{', '}'); bcheck2(brackcnt, '[', ']'); bcheck2(parencnt, '(', ')'); } void bcheck2(int n, int c1, int c2) { if (n == 1) fprintf(stderr, "\tmissing %c\n", c2); else if (n > 1) fprintf(stderr, "\t%d missing %c's\n", n, c2); else if (n == -1) fprintf(stderr, "\textra %c\n", c2); else if (n < -1) fprintf(stderr, "\t%d extra %c's\n", -n, c2); } void FATAL(const char *fmt, ...) { extern char *cmdname; va_list varg; fflush(stdout); fprintf(stderr, "%s: ", cmdname); va_start(varg, fmt); vfprintf(stderr, fmt, varg); va_end(varg); error(); if (dbg > 1) /* core dump if serious debugging on */ abort(); exit(2); } void WARNING(const char *fmt, ...) { extern char *cmdname; va_list varg; fflush(stdout); fprintf(stderr, "%s: ", cmdname); va_start(varg, fmt); vfprintf(stderr, fmt, varg); va_end(varg); error(); } void error() { extern Node *curnode; fprintf(stderr, "\n"); if (compile_time != 2 && NR && *NR > 0) { fprintf(stderr, " input record number %d", (int) (*FNR)); if (strcmp(*FILENAME, "-") != 0) fprintf(stderr, ", file %s", *FILENAME); fprintf(stderr, "\n"); } if (compile_time != 2 && curnode) fprintf(stderr, " source line number %d", curnode->lineno); else if (compile_time != 2 && lineno) fprintf(stderr, " source line number %d", lineno); if (compile_time == 1 && cursource() != NULL) fprintf(stderr, " source file %s", cursource()); fprintf(stderr, "\n"); eprint(); } void eprint(void) /* try to print context around error */ { char *p, *q; int c; static int been_here = 0; extern char ebuf[], *ep; if (compile_time == 2 || compile_time == 0 || been_here++ > 0) return; p = ep - 1; if (p > ebuf && *p == '\n') p--; for ( ; p > ebuf && *p != '\n' && *p != '\0'; p--) ; while (*p == '\n') p++; fprintf(stderr, " context is\n\t"); for (q=ep-1; q>=p && *q!=' ' && *q!='\t' && *q!='\n'; q--) ; for ( ; p < q; p++) if (*p) putc(*p, stderr); fprintf(stderr, " >>> "); for ( ; p < ep; p++) if (*p) putc(*p, stderr); fprintf(stderr, " <<< "); if (*ep) while ((c = input()) != '\n' && c != '\0' && c != EOF) { putc(c, stderr); bclass(c); } putc('\n', stderr); ep = ebuf; } void bclass(int c) { switch (c) { case '{': bracecnt++; break; case '}': bracecnt--; break; case '[': brackcnt++; break; case ']': brackcnt--; break; case '(': parencnt++; break; case ')': parencnt--; break; } } double errcheck(double x, const char *s) { if (errno == EDOM) { errno = 0; WARNING("%s argument out of domain", s); x = 1; } else if (errno == ERANGE) { errno = 0; WARNING("%s result out of range", s); x = 1; } return x; } int isclvar(const char *s) /* is s of form var=something ? */ { const char *os = s; if (!isalpha((uschar) *s) && *s != '_') return 0; for ( ; *s; s++) if (!(isalnum((uschar) *s) || *s == '_')) break; return *s == '=' && s > os && *(s+1) != '='; } /* strtod is supposed to be a proper test of what's a valid number */ /* appears to be broken in gcc on linux: thinks 0x123 is a valid FP number */ /* wrong: violates 4.10.1.4 of ansi C standard */ #include int is_number(const char *s) { double r; char *ep; errno = 0; r = strtod(s, &ep); if (ep == s || r == HUGE_VAL || errno == ERANGE) return 0; while (*ep == ' ' || *ep == '\t' || *ep == '\n') ep++; if (*ep == '\0') return 1; else return 0; } bioawk-1.0/main.c000066400000000000000000000145551220715177100137330ustar00rootroot00000000000000/**************************************************************** Copyright (C) Lucent Technologies 1997 All Rights Reserved Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that the copyright notice and this permission notice and warranty disclaimer appear in supporting documentation, and that the name Lucent Technologies or any of its entities not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ****************************************************************/ const char *version = "version 20110810"; #define DEBUG #include #include #include #include #include #include #include "awk.h" #include "ytab.h" extern char **environ; extern int nfields; int dbg = 0; Awkfloat srand_seed = 1; char *cmdname; /* gets argv[0] for error messages */ extern FILE *yyin; /* lex input file */ char *lexprog; /* points to program argument if it exists */ extern int errorflag; /* non-zero if any syntax errors; set by yyerror */ int compile_time = 2; /* for error printing: */ /* 2 = cmdline, 1 = compile, 0 = running */ #define MAX_PFILE 20 /* max number of -f's */ char *pfile[MAX_PFILE]; /* program filenames from -f's */ int npfile = 0; /* number of filenames */ int curpfile = 0; /* current filename */ int safe = 0; /* 1 => "safe" mode */ int main(int argc, char *argv[]) { const char *fs = NULL; char tmp[16]; setlocale(LC_CTYPE, ""); setlocale(LC_NUMERIC, "C"); /* for parsing cmdline & prog */ cmdname = argv[0]; if (argc == 1) { fprintf(stderr, "usage: %s [-F fs] [-v var=value] [-c fmt] [-tH] [-f progfile | 'prog'] [file ...]\n", cmdname); exit(1); } signal(SIGFPE, fpecatch); srand_seed = 1; srand(srand_seed); yyin = NULL; symtab = makesymtab(NSYMTAB/NSYMTAB); while (argc > 1 && argv[1][0] == '-' && argv[1][1] != '\0') { if (strcmp(argv[1],"-version") == 0 || strcmp(argv[1],"--version") == 0) { printf("awk %s\n", version); exit(0); break; } if (strncmp(argv[1], "--", 2) == 0) { /* explicit end of args */ argc--; argv++; break; } switch (argv[1][1]) { case 's': if (strcmp(argv[1], "-safe") == 0) safe = 1; break; case 'f': /* next argument is program filename */ if (argv[1][2] != 0) { /* arg is -fsomething */ if (npfile >= MAX_PFILE - 1) FATAL("too many -f options"); pfile[npfile++] = &argv[1][2]; } else { /* arg is -f something */ argc--; argv++; if (argc <= 1) FATAL("no program filename"); if (npfile >= MAX_PFILE - 1) FATAL("too many -f options"); pfile[npfile++] = argv[1]; } break; case 'F': /* set field separator */ if (argv[1][2] != 0) { /* arg is -Fsomething */ if (argv[1][2] == 't' && argv[1][3] == 0) /* wart: t=>\t */ fs = "\t"; else if (argv[1][2] != 0) fs = &argv[1][2]; } else { /* arg is -F something */ argc--; argv++; if (argc > 1 && argv[1][0] == 't' && argv[1][1] == 0) /* wart: t=>\t */ fs = "\t"; else if (argc > 1 && argv[1][0] != 0) fs = &argv[1][0]; } if (fs == NULL || *fs == '\0') WARNING("field separator FS is empty"); break; case 't': strcpy(tmp, "FS=\\t"); setclvar(tmp); strcpy(tmp, "OFS=\\t"); setclvar(tmp); break; case 'v': /* -v a=1 to be done NOW. one -v for each */ if (argv[1][2] != 0) { /* arg is -vsomething */ if (isclvar(&argv[1][2])) setclvar(&argv[1][2]); else FATAL("invalid -v option argument: %s", &argv[1][2]); } else { /* arg is -v something */ argc--; argv++; if (argc <= 1) FATAL("no variable name"); if (isclvar(argv[1])) setclvar(argv[1]); else FATAL("invalid -v option argument: %s", argv[1]); } break; case 'd': dbg = atoi(&argv[1][2]); if (dbg == 0) dbg = 1; printf("awk %s\n", version); break; case 'H': bio_flag |= BIO_SHOW_HDR; break; case 'c': if (argv[1][2] != 0) { /* arg is -csomething */ if ((bio_fmt = bio_get_fmt(&argv[1][2])) == BIO_NULL) return 1; } else { /* arg is -c something */ argc--; argv++; if (argc <= 1) FATAL("no variable name"); if ((bio_fmt = bio_get_fmt(argv[1])) == BIO_NULL) return 1; } break; default: WARNING("unknown option %s ignored", argv[1]); break; } if ((argv[1][1] == 't' || argv[1][1] == 'H') && argv[1][2] != 0) { /* dealing with for example "-tc help" */ char *p; for (p = &argv[1][2]; *p; ++p) *(p-1) = *p; *(p-1) = *p; } else --argc, ++argv; } /* argv[1] is now the first argument */ if (npfile == 0) { /* no -f; first argument is program */ if (argc <= 1) { if (dbg) exit(0); FATAL("no program given"); } dprintf( ("program = |%s|\n", argv[1]) ); lexprog = argv[1]; argc--; argv++; } recinit(recsize); syminit(); compile_time = 1; argv[0] = cmdname; /* put prog name at front of arglist */ dprintf( ("argc=%d, argv[0]=%s\n", argc, argv[0]) ); arginit(argc, argv); if (!safe) envinit(environ); yyparse(); setlocale(LC_NUMERIC, ""); /* back to whatever it is locally */ if (fs) *FS = qstring(fs, '\0'); dprintf( ("errorflag=%d\n", errorflag) ); if (errorflag == 0) { compile_time = 0; run(winner); } else bracecheck(); return(errorflag); } int pgetc(void) /* get 1 character from awk program */ { int c; for (;;) { if (yyin == NULL) { if (curpfile >= npfile) return EOF; if (strcmp(pfile[curpfile], "-") == 0) yyin = stdin; else if ((yyin = fopen(pfile[curpfile], "r")) == NULL) FATAL("can't open file %s", pfile[curpfile]); lineno = 1; } if ((c = getc(yyin)) != EOF) return c; if (yyin != stdin) fclose(yyin); yyin = NULL; curpfile++; } } char *cursource(void) /* current source file name */ { if (npfile > 0) return pfile[curpfile]; else return NULL; } bioawk-1.0/maketab.c000066400000000000000000000120221220715177100143760ustar00rootroot00000000000000/**************************************************************** Copyright (C) Lucent Technologies 1997 All Rights Reserved Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that the copyright notice and this permission notice and warranty disclaimer appear in supporting documentation, and that the name Lucent Technologies or any of its entities not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ****************************************************************/ /* * this program makes the table to link function names * and type indices that is used by execute() in run.c. * it finds the indices in ytab.h, produced by yacc. */ #include #include #include #include "awk.h" #include "ytab.h" struct xx { int token; const char *name; const char *pname; } proc[] = { { PROGRAM, "program", NULL }, { BOR, "boolop", " || " }, { AND, "boolop", " && " }, { NOT, "boolop", " !" }, { NE, "relop", " != " }, { EQ, "relop", " == " }, { LE, "relop", " <= " }, { LT, "relop", " < " }, { GE, "relop", " >= " }, { GT, "relop", " > " }, { ARRAY, "array", NULL }, { INDIRECT, "indirect", "$(" }, { SUBSTR, "substr", "substr" }, { SUB, "sub", "sub" }, { GSUB, "gsub", "gsub" }, { INDEX, "sindex", "sindex" }, { SPRINTF, "awksprintf", "sprintf " }, { ADD, "arith", " + " }, { MINUS, "arith", " - " }, { MULT, "arith", " * " }, { DIVIDE, "arith", " / " }, { MOD, "arith", " % " }, { UMINUS, "arith", " -" }, { POWER, "arith", " **" }, { PREINCR, "incrdecr", "++" }, { POSTINCR, "incrdecr", "++" }, { PREDECR, "incrdecr", "--" }, { POSTDECR, "incrdecr", "--" }, { CAT, "cat", " " }, { PASTAT, "pastat", NULL }, { PASTAT2, "dopa2", NULL }, { MATCH, "matchop", " ~ " }, { NOTMATCH, "matchop", " !~ " }, { MATCHFCN, "matchop", "matchop" }, { INTEST, "intest", "intest" }, { PRINTF, "awkprintf", "printf" }, { PRINT, "printstat", "print" }, { CLOSE, "closefile", "closefile" }, { DELETE, "awkdelete", "awkdelete" }, { SPLIT, "split", "split" }, { ASSIGN, "assign", " = " }, { ADDEQ, "assign", " += " }, { SUBEQ, "assign", " -= " }, { MULTEQ, "assign", " *= " }, { DIVEQ, "assign", " /= " }, { MODEQ, "assign", " %= " }, { POWEQ, "assign", " ^= " }, { CONDEXPR, "condexpr", " ?: " }, { IF, "ifstat", "if(" }, { WHILE, "whilestat", "while(" }, { FOR, "forstat", "for(" }, { DO, "dostat", "do" }, { IN, "instat", "instat" }, { NEXT, "jump", "next" }, { NEXTFILE, "jump", "nextfile" }, { EXIT, "jump", "exit" }, { BREAK, "jump", "break" }, { CONTINUE, "jump", "continue" }, { RETURN, "jump", "ret" }, { BLTIN, "bltin", "bltin" }, { CALL, "call", "call" }, { ARG, "arg", "arg" }, { VARNF, "getnf", "NF" }, { GETLINE, "awkgetline", "getline" }, { 0, "", "" }, }; #define SIZE (LASTTOKEN - FIRSTTOKEN + 1) const char *table[SIZE]; char *names[SIZE]; int main(int argc, char *argv[]) { const struct xx *p; int i, n, tok; char c; FILE *fp; char buf[200], name[200], def[200]; printf("#include \n"); printf("#include \"awk.h\"\n"); printf("#include \"ytab.h\"\n\n"); for (i = SIZE; --i >= 0; ) names[i] = ""; if ((fp = fopen("ytab.h", "r")) == NULL) { fprintf(stderr, "maketab can't open ytab.h!\n"); exit(1); } printf("static char *printname[%d] = {\n", SIZE); i = 0; while (fgets(buf, sizeof buf, fp) != NULL) { n = sscanf(buf, "%1c %s %s %d", &c, def, name, &tok); if (c != '#' || (n != 4 && strcmp(def,"define") != 0)) /* not a valid #define */ continue; if (tok < FIRSTTOKEN || tok > LASTTOKEN) { /* fprintf(stderr, "maketab funny token %d %s ignored\n", tok, buf); */ continue; } names[tok-FIRSTTOKEN] = (char *) malloc(strlen(name)+1); strcpy(names[tok-FIRSTTOKEN], name); printf("\t(char *) \"%s\",\t/* %d */\n", name, tok); i++; } printf("};\n\n"); for (p=proc; p->token!=0; p++) table[p->token-FIRSTTOKEN] = p->name; printf("\nCell *(*proctab[%d])(Node **, int) = {\n", SIZE); for (i=0; i LASTTOKEN) {\n"); printf(" sprintf(buf, \"token %%d\", n);\n"); printf(" return buf;\n"); printf(" }\n"); printf(" return printname[n-FIRSTTOKEN];\n"); printf("}\n"); return 0; } bioawk-1.0/parse.c000066400000000000000000000121011220715177100141020ustar00rootroot00000000000000/**************************************************************** Copyright (C) Lucent Technologies 1997 All Rights Reserved Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that the copyright notice and this permission notice and warranty disclaimer appear in supporting documentation, and that the name Lucent Technologies or any of its entities not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ****************************************************************/ #define DEBUG #include #include #include #include "awk.h" #include "ytab.h" Node *nodealloc(int n) { Node *x; x = (Node *) malloc(sizeof(Node) + (n-1)*sizeof(Node *)); if (x == NULL) FATAL("out of space in nodealloc"); x->nnext = NULL; x->lineno = lineno; return(x); } Node *exptostat(Node *a) { a->ntype = NSTAT; return(a); } Node *node1(int a, Node *b) { Node *x; x = nodealloc(1); x->nobj = a; x->narg[0]=b; return(x); } Node *node2(int a, Node *b, Node *c) { Node *x; x = nodealloc(2); x->nobj = a; x->narg[0] = b; x->narg[1] = c; return(x); } Node *node3(int a, Node *b, Node *c, Node *d) { Node *x; x = nodealloc(3); x->nobj = a; x->narg[0] = b; x->narg[1] = c; x->narg[2] = d; return(x); } Node *node4(int a, Node *b, Node *c, Node *d, Node *e) { Node *x; x = nodealloc(4); x->nobj = a; x->narg[0] = b; x->narg[1] = c; x->narg[2] = d; x->narg[3] = e; return(x); } Node *stat1(int a, Node *b) { Node *x; x = node1(a,b); x->ntype = NSTAT; return(x); } Node *stat2(int a, Node *b, Node *c) { Node *x; x = node2(a,b,c); x->ntype = NSTAT; return(x); } Node *stat3(int a, Node *b, Node *c, Node *d) { Node *x; x = node3(a,b,c,d); x->ntype = NSTAT; return(x); } Node *stat4(int a, Node *b, Node *c, Node *d, Node *e) { Node *x; x = node4(a,b,c,d,e); x->ntype = NSTAT; return(x); } Node *op1(int a, Node *b) { Node *x; x = node1(a,b); x->ntype = NEXPR; return(x); } Node *op2(int a, Node *b, Node *c) { Node *x; x = node2(a,b,c); x->ntype = NEXPR; return(x); } Node *op3(int a, Node *b, Node *c, Node *d) { Node *x; x = node3(a,b,c,d); x->ntype = NEXPR; return(x); } Node *op4(int a, Node *b, Node *c, Node *d, Node *e) { Node *x; x = node4(a,b,c,d,e); x->ntype = NEXPR; return(x); } Node *celltonode(Cell *a, int b) { Node *x; a->ctype = OCELL; a->csub = b; x = node1(0, (Node *) a); x->ntype = NVALUE; return(x); } Node *rectonode(void) /* make $0 into a Node */ { extern Cell *literal0; return op1(INDIRECT, celltonode(literal0, CUNK)); } Node *makearr(Node *p) { Cell *cp; if (isvalue(p)) { cp = (Cell *) (p->narg[0]); if (isfcn(cp)) SYNTAX( "%s is a function, not an array", cp->nval ); else if (!isarr(cp)) { xfree(cp->sval); cp->sval = (char *) makesymtab(NSYMTAB); cp->tval = ARR; } } return p; } #define PA2NUM 50 /* max number of pat,pat patterns allowed */ int paircnt; /* number of them in use */ int pairstack[PA2NUM]; /* state of each pat,pat */ Node *pa2stat(Node *a, Node *b, Node *c) /* pat, pat {...} */ { Node *x; x = node4(PASTAT2, a, b, c, itonp(paircnt)); if (paircnt++ >= PA2NUM) SYNTAX( "limited to %d pat,pat statements", PA2NUM ); x->ntype = NSTAT; return(x); } Node *linkum(Node *a, Node *b) { Node *c; if (errorflag) /* don't link things that are wrong */ return a; if (a == NULL) return(b); else if (b == NULL) return(a); for (c = a; c->nnext != NULL; c = c->nnext) ; c->nnext = b; return(a); } void defn(Cell *v, Node *vl, Node *st) /* turn on FCN bit in definition, */ { /* body of function, arglist */ Node *p; int n; if (isarr(v)) { SYNTAX( "`%s' is an array name and a function name", v->nval ); return; } if (isarg(v->nval) != -1) { SYNTAX( "`%s' is both function name and argument name", v->nval ); return; } v->tval = FCN; v->sval = (char *) st; n = 0; /* count arguments */ for (p = vl; p; p = p->nnext) n++; v->fval = n; dprintf( ("defining func %s (%d args)\n", v->nval, n) ); } int isarg(const char *s) /* is s in argument list for current function? */ { /* return -1 if not, otherwise arg # */ extern Node *arglist; Node *p = arglist; int n; for (n = 0; p != 0; p = p->nnext, n++) if (strcmp(((Cell *)(p->narg[0]))->nval, s) == 0) return n; return -1; } int ptoi(void *p) /* convert pointer to integer */ { return (int) (long) p; /* swearing that p fits, of course */ } Node *itonp(int i) /* and vice versa */ { return (Node *) (long) i; } bioawk-1.0/proto.h000066400000000000000000000153131220715177100141500ustar00rootroot00000000000000/**************************************************************** Copyright (C) Lucent Technologies 1997 All Rights Reserved Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that the copyright notice and this permission notice and warranty disclaimer appear in supporting documentation, and that the name Lucent Technologies or any of its entities not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ****************************************************************/ extern int yywrap(void); extern void setfname(Cell *); extern int constnode(Node *); extern char *strnode(Node *); extern Node *notnull(Node *); extern int yyparse(void); extern int yylex(void); extern void startreg(void); extern int input(void); extern void unput(int); extern void unputstr(const char *); extern int yylook(void); extern int yyback(int *, int); extern int yyinput(void); extern fa *makedfa(const char *, int); extern fa *mkdfa(const char *, int); extern int makeinit(fa *, int); extern void penter(Node *); extern void freetr(Node *); extern int hexstr(uschar **); extern int quoted(uschar **); extern char *cclenter(const char *); extern void overflo(const char *); extern void cfoll(fa *, Node *); extern int first(Node *); extern void follow(Node *); extern int member(int, const char *); extern int match(fa *, const char *); extern int pmatch(fa *, const char *); extern int nematch(fa *, const char *); extern Node *reparse(const char *); extern Node *regexp(void); extern Node *primary(void); extern Node *concat(Node *); extern Node *alt(Node *); extern Node *unary(Node *); extern int relex(void); extern int cgoto(fa *, int, int); extern void freefa(fa *); extern int pgetc(void); extern char *cursource(void); extern Node *nodealloc(int); extern Node *exptostat(Node *); extern Node *node1(int, Node *); extern Node *node2(int, Node *, Node *); extern Node *node3(int, Node *, Node *, Node *); extern Node *node4(int, Node *, Node *, Node *, Node *); extern Node *stat3(int, Node *, Node *, Node *); extern Node *op2(int, Node *, Node *); extern Node *op1(int, Node *); extern Node *stat1(int, Node *); extern Node *op3(int, Node *, Node *, Node *); extern Node *op4(int, Node *, Node *, Node *, Node *); extern Node *stat2(int, Node *, Node *); extern Node *stat4(int, Node *, Node *, Node *, Node *); extern Node *celltonode(Cell *, int); extern Node *rectonode(void); extern Node *makearr(Node *); extern Node *pa2stat(Node *, Node *, Node *); extern Node *linkum(Node *, Node *); extern void defn(Cell *, Node *, Node *); extern int isarg(const char *); extern char *tokname(int); extern Cell *(*proctab[])(Node **, int); extern int ptoi(void *); extern Node *itonp(int); extern void syminit(void); extern void arginit(int, char **); extern void envinit(char **); extern Array *makesymtab(int); extern void freesymtab(Cell *); extern void freeelem(Cell *, const char *); extern Cell *setsymtab(const char *, const char *, double, unsigned int, Array *); extern int hash(const char *, int); extern void rehash(Array *); extern Cell *lookup(const char *, Array *); extern double setfval(Cell *, double); extern void funnyvar(Cell *, const char *); extern char *setsval(Cell *, const char *); extern double getfval(Cell *); extern char *getsval(Cell *); extern char *getpssval(Cell *); /* for print */ extern char *tostring(const char *); extern char *qstring(const char *, int); extern void recinit(unsigned int); extern void initgetrec(void); extern void makefields(int, int); extern void growfldtab(int n); extern int getrec(char **, int *, int); extern void nextfile(void); extern int readrec(char **buf, int *bufsize, FILE *inf); extern char *getargv(int); extern void setclvar(char *); extern void fldbld(void); extern void cleanfld(int, int); extern void newfld(int); extern int refldbld(const char *, const char *); extern void recbld(void); extern Cell *fieldadr(int); extern void yyerror(const char *); extern void fpecatch(int); extern void bracecheck(void); extern void bcheck2(int, int, int); extern void SYNTAX(const char *, ...); extern void FATAL(const char *, ...); extern void WARNING(const char *, ...); extern void error(void); extern void eprint(void); extern void bclass(int); extern double errcheck(double, const char *); extern int isclvar(const char *); extern int is_number(const char *); extern int adjbuf(char **pb, int *sz, int min, int q, char **pbp, const char *what); extern void run(Node *); extern Cell *execute(Node *); extern Cell *program(Node **, int); extern Cell *call(Node **, int); extern Cell *copycell(Cell *); extern Cell *arg(Node **, int); extern Cell *jump(Node **, int); extern Cell *awkgetline(Node **, int); extern Cell *getnf(Node **, int); extern Cell *array(Node **, int); extern Cell *awkdelete(Node **, int); extern Cell *intest(Node **, int); extern Cell *matchop(Node **, int); extern Cell *boolop(Node **, int); extern Cell *relop(Node **, int); extern void tfree(Cell *); extern Cell *gettemp(void); extern Cell *field(Node **, int); extern Cell *indirect(Node **, int); extern Cell *substr(Node **, int); extern Cell *sindex(Node **, int); extern int format(char **, int *, const char *, Node *); extern Cell *awksprintf(Node **, int); extern Cell *awkprintf(Node **, int); extern Cell *arith(Node **, int); extern double ipow(double, int); extern Cell *incrdecr(Node **, int); extern Cell *assign(Node **, int); extern Cell *cat(Node **, int); extern Cell *pastat(Node **, int); extern Cell *dopa2(Node **, int); extern Cell *split(Node **, int); extern Cell *condexpr(Node **, int); extern Cell *ifstat(Node **, int); extern Cell *whilestat(Node **, int); extern Cell *dostat(Node **, int); extern Cell *forstat(Node **, int); extern Cell *instat(Node **, int); extern Cell *bltin(Node **, int); extern Cell *printstat(Node **, int); extern Cell *nullproc(Node **, int); extern FILE *redirect(int, Node *); extern FILE *openfile(int, const char *); extern const char *filename(FILE *); extern Cell *closefile(Node **, int); extern void closeall(void); extern Cell *sub(Node **, int); extern Cell *gsub(Node **, int); extern FILE *popen(const char *, const char *); extern int pclose(FILE *); bioawk-1.0/run.c000066400000000000000000001276521220715177100136160ustar00rootroot00000000000000/**************************************************************** Copyright (C) Lucent Technologies 1997 All Rights Reserved Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that the copyright notice and this permission notice and warranty disclaimer appear in supporting documentation, and that the name Lucent Technologies or any of its entities not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ****************************************************************/ #define DEBUG #include #include #include #include #include #include #include #include #include "awk.h" #include "ytab.h" #define tempfree(x) if (istemp(x)) tfree(x); else /* #undef tempfree void tempfree(Cell *p) { if (p->ctype == OCELL && (p->csub < CUNK || p->csub > CFREE)) { WARNING("bad csub %d in Cell %d %s", p->csub, p->ctype, p->sval); } if (istemp(p)) tfree(p); } */ /* do we really need these? */ /* #ifdef _NFILE */ /* #ifndef FOPEN_MAX */ /* #define FOPEN_MAX _NFILE */ /* #endif */ /* #endif */ /* */ /* #ifndef FOPEN_MAX */ /* #define FOPEN_MAX 40 */ /* max number of open files */ /* #endif */ /* */ /* #ifndef RAND_MAX */ /* #define RAND_MAX 32767 */ /* all that ansi guarantees */ /* #endif */ jmp_buf env; extern int pairstack[]; extern Awkfloat srand_seed; Node *winner = NULL; /* root of parse tree */ Cell *tmps; /* free temporary cells for execution */ static Cell truecell ={ OBOOL, BTRUE, 0, 0, 1.0, NUM }; Cell *True = &truecell; static Cell falsecell ={ OBOOL, BFALSE, 0, 0, 0.0, NUM }; Cell *False = &falsecell; static Cell breakcell ={ OJUMP, JBREAK, 0, 0, 0.0, NUM }; Cell *jbreak = &breakcell; static Cell contcell ={ OJUMP, JCONT, 0, 0, 0.0, NUM }; Cell *jcont = &contcell; static Cell nextcell ={ OJUMP, JNEXT, 0, 0, 0.0, NUM }; Cell *jnext = &nextcell; static Cell nextfilecell ={ OJUMP, JNEXTFILE, 0, 0, 0.0, NUM }; Cell *jnextfile = &nextfilecell; static Cell exitcell ={ OJUMP, JEXIT, 0, 0, 0.0, NUM }; Cell *jexit = &exitcell; static Cell retcell ={ OJUMP, JRET, 0, 0, 0.0, NUM }; Cell *jret = &retcell; static Cell tempcell ={ OCELL, CTEMP, 0, "", 0.0, NUM|STR|DONTFREE }; Node *curnode = NULL; /* the node being executed, for debugging */ /* buffer memory management */ int adjbuf(char **pbuf, int *psiz, int minlen, int quantum, char **pbptr, const char *whatrtn) /* pbuf: address of pointer to buffer being managed * psiz: address of buffer size variable * minlen: minimum length of buffer needed * quantum: buffer size quantum * pbptr: address of movable pointer into buffer, or 0 if none * whatrtn: name of the calling routine if failure should cause fatal error * * return 0 for realloc failure, !=0 for success */ { if (minlen > *psiz) { char *tbuf; int rminlen = quantum ? minlen % quantum : 0; int boff = pbptr ? *pbptr - *pbuf : 0; /* round up to next multiple of quantum */ if (rminlen) minlen += quantum - rminlen; tbuf = (char *) realloc(*pbuf, minlen); dprintf( ("adjbuf %s: %d %d (pbuf=%p, tbuf=%p)\n", whatrtn, *psiz, minlen, *pbuf, tbuf) ); if (tbuf == NULL) { if (whatrtn) FATAL("out of memory in %s", whatrtn); return 0; } *pbuf = tbuf; *psiz = minlen; if (pbptr) *pbptr = tbuf + boff; } return 1; } void run(Node *a) /* execution of parse tree starts here */ { extern void stdinit(void); stdinit(); execute(a); closeall(); } Cell *execute(Node *u) /* execute a node of the parse tree */ { Cell *(*proc)(Node **, int); Cell *x; Node *a; if (u == NULL) return(True); for (a = u; ; a = a->nnext) { curnode = a; if (isvalue(a)) { x = (Cell *) (a->narg[0]); if (isfld(x) && !donefld) fldbld(); else if (isrec(x) && !donerec) recbld(); return(x); } if (notlegal(a->nobj)) /* probably a Cell* but too risky to print */ FATAL("illegal statement"); proc = proctab[a->nobj-FIRSTTOKEN]; x = (*proc)(a->narg, a->nobj); if (isfld(x) && !donefld) fldbld(); else if (isrec(x) && !donerec) recbld(); if (isexpr(a)) return(x); if (isjump(x)) return(x); if (a->nnext == NULL) return(x); tempfree(x); } } Cell *program(Node **a, int n) /* execute an awk program */ { /* a[0] = BEGIN, a[1] = body, a[2] = END */ Cell *x; if (setjmp(env) != 0) goto ex; if (a[0]) { /* BEGIN */ x = execute(a[0]); if (isexit(x)) return(True); if (isjump(x)) FATAL("illegal break, continue, next or nextfile from BEGIN"); tempfree(x); } if (a[1] || a[2]) { if (bio_fmt > BIO_HDR) bio_set_colnm(); while (getrec(&record, &recsize, 1) > 0) { if (bio_skip_hdr(record)) continue; if (bio_fmt == BIO_HDR && (int)(*NR + .499) == 1) bio_set_colnm(); x = execute(a[1]); if (isexit(x)) break; tempfree(x); } } ex: if (setjmp(env) != 0) /* handles exit within END */ goto ex1; if (a[2]) { /* END */ x = execute(a[2]); if (isbreak(x) || isnext(x) || iscont(x)) FATAL("illegal break, continue, next or nextfile from END"); tempfree(x); } ex1: return(True); } struct Frame { /* stack frame for awk function calls */ int nargs; /* number of arguments in this call */ Cell *fcncell; /* pointer to Cell for function */ Cell **args; /* pointer to array of arguments after execute */ Cell *retval; /* return value */ }; #define NARGS 50 /* max args in a call */ struct Frame *frame = NULL; /* base of stack frames; dynamically allocated */ int nframe = 0; /* number of frames allocated */ struct Frame *fp = NULL; /* frame pointer. bottom level unused */ Cell *call(Node **a, int n) /* function call. very kludgy and fragile */ { static Cell newcopycell = { OCELL, CCOPY, 0, "", 0.0, NUM|STR|DONTFREE }; int i, ncall, ndef; int freed = 0; /* handles potential double freeing when fcn & param share a tempcell */ Node *x; Cell *args[NARGS], *oargs[NARGS]; /* BUG: fixed size arrays */ Cell *y, *z, *fcn; char *s; fcn = execute(a[0]); /* the function itself */ s = fcn->nval; if (!isfcn(fcn)) FATAL("calling undefined function %s", s); if (frame == NULL) { fp = frame = (struct Frame *) calloc(nframe += 100, sizeof(struct Frame)); if (frame == NULL) FATAL("out of space for stack frames calling %s", s); } for (ncall = 0, x = a[1]; x != NULL; x = x->nnext) /* args in call */ ncall++; ndef = (int) fcn->fval; /* args in defn */ dprintf( ("calling %s, %d args (%d in defn), fp=%d\n", s, ncall, ndef, (int) (fp-frame)) ); if (ncall > ndef) WARNING("function %s called with %d args, uses only %d", s, ncall, ndef); if (ncall + ndef > NARGS) FATAL("function %s has %d arguments, limit %d", s, ncall+ndef, NARGS); for (i = 0, x = a[1]; x != NULL; i++, x = x->nnext) { /* get call args */ dprintf( ("evaluate args[%d], fp=%d:\n", i, (int) (fp-frame)) ); y = execute(x); oargs[i] = y; dprintf( ("args[%d]: %s %f <%s>, t=%o\n", i, NN(y->nval), y->fval, isarr(y) ? "(array)" : NN(y->sval), y->tval) ); if (isfcn(y)) FATAL("can't use function %s as argument in %s", y->nval, s); if (isarr(y)) args[i] = y; /* arrays by ref */ else args[i] = copycell(y); tempfree(y); } for ( ; i < ndef; i++) { /* add null args for ones not provided */ args[i] = gettemp(); *args[i] = newcopycell; } fp++; /* now ok to up frame */ if (fp >= frame + nframe) { int dfp = fp - frame; /* old index */ frame = (struct Frame *) realloc((char *) frame, (nframe += 100) * sizeof(struct Frame)); if (frame == NULL) FATAL("out of space for stack frames in %s", s); fp = frame + dfp; } fp->fcncell = fcn; fp->args = args; fp->nargs = ndef; /* number defined with (excess are locals) */ fp->retval = gettemp(); dprintf( ("start exec of %s, fp=%d\n", s, (int) (fp-frame)) ); y = execute((Node *)(fcn->sval)); /* execute body */ dprintf( ("finished exec of %s, fp=%d\n", s, (int) (fp-frame)) ); for (i = 0; i < ndef; i++) { Cell *t = fp->args[i]; if (isarr(t)) { if (t->csub == CCOPY) { if (i >= ncall) { freesymtab(t); t->csub = CTEMP; tempfree(t); } else { oargs[i]->tval = t->tval; oargs[i]->tval &= ~(STR|NUM|DONTFREE); oargs[i]->sval = t->sval; tempfree(t); } } } else if (t != y) { /* kludge to prevent freeing twice */ t->csub = CTEMP; tempfree(t); } else if (t == y && t->csub == CCOPY) { t->csub = CTEMP; tempfree(t); freed = 1; } } tempfree(fcn); if (isexit(y) || isnext(y)) return y; if (freed == 0) { tempfree(y); /* don't free twice! */ } z = fp->retval; /* return value */ dprintf( ("%s returns %g |%s| %o\n", s, getfval(z), getsval(z), z->tval) ); fp--; return(z); } Cell *copycell(Cell *x) /* make a copy of a cell in a temp */ { Cell *y; y = gettemp(); y->csub = CCOPY; /* prevents freeing until call is over */ y->nval = x->nval; /* BUG? */ if (isstr(x)) y->sval = tostring(x->sval); y->fval = x->fval; y->tval = x->tval & ~(CON|FLD|REC|DONTFREE); /* copy is not constant or field */ /* is DONTFREE right? */ return y; } Cell *arg(Node **a, int n) /* nth argument of a function */ { n = ptoi(a[0]); /* argument number, counting from 0 */ dprintf( ("arg(%d), fp->nargs=%d\n", n, fp->nargs) ); if (n+1 > fp->nargs) FATAL("argument #%d of function %s was not supplied", n+1, fp->fcncell->nval); return fp->args[n]; } Cell *jump(Node **a, int n) /* break, continue, next, nextfile, return */ { Cell *y; switch (n) { case EXIT: if (a[0] != NULL) { y = execute(a[0]); errorflag = (int) getfval(y); tempfree(y); } longjmp(env, 1); case RETURN: if (a[0] != NULL) { y = execute(a[0]); if ((y->tval & (STR|NUM)) == (STR|NUM)) { setsval(fp->retval, getsval(y)); fp->retval->fval = getfval(y); fp->retval->tval |= NUM; } else if (y->tval & STR) setsval(fp->retval, getsval(y)); else if (y->tval & NUM) setfval(fp->retval, getfval(y)); else /* can't happen */ FATAL("bad type variable %d", y->tval); tempfree(y); } return(jret); case NEXT: return(jnext); case NEXTFILE: nextfile(); return(jnextfile); case BREAK: return(jbreak); case CONTINUE: return(jcont); default: /* can't happen */ FATAL("illegal jump type %d", n); } return 0; /* not reached */ } Cell *awkgetline(Node **a, int n) /* get next line from specific input */ { /* a[0] is variable, a[1] is operator, a[2] is filename */ Cell *r, *x; extern Cell **fldtab; FILE *fp; char *buf; int bufsize = recsize; int mode; if ((buf = (char *) malloc(bufsize)) == NULL) FATAL("out of memory in getline"); fflush(stdout); /* in case someone is waiting for a prompt */ r = gettemp(); if (a[1] != NULL) { /* getline < file */ x = execute(a[2]); /* filename */ mode = ptoi(a[1]); if (mode == '|') /* input pipe */ mode = LE; /* arbitrary flag */ fp = openfile(mode, getsval(x)); tempfree(x); if (fp == NULL) n = -1; else n = readrec(&buf, &bufsize, fp); if (n <= 0) { ; } else if (a[0] != NULL) { /* getline var sval)) { fldtab[0]->fval = atof(fldtab[0]->sval); fldtab[0]->tval |= NUM; } } } else { /* bare getline; use current input */ if (a[0] == NULL) /* getline */ n = getrec(&record, &recsize, 1); else { /* getline var */ n = getrec(&buf, &bufsize, 0); x = execute(a[0]); setsval(x, buf); tempfree(x); } } setfval(r, (Awkfloat) n); free(buf); return r; } Cell *getnf(Node **a, int n) /* get NF */ { if (donefld == 0) fldbld(); return (Cell *) a[0]; } Cell *array(Node **a, int n) /* a[0] is symtab, a[1] is list of subscripts */ { Cell *x, *y, *z; char *s; Node *np; char *buf; int bufsz = recsize; int nsub = strlen(*SUBSEP); if ((buf = (char *) malloc(bufsz)) == NULL) FATAL("out of memory in array"); x = execute(a[0]); /* Cell* for symbol table */ buf[0] = 0; for (np = a[1]; np; np = np->nnext) { y = execute(np); /* subscript */ s = getsval(y); if (!adjbuf(&buf, &bufsz, strlen(buf)+strlen(s)+nsub+1, recsize, 0, "array")) FATAL("out of memory for %s[%s...]", x->nval, buf); strcat(buf, s); if (np->nnext) strcat(buf, *SUBSEP); tempfree(y); } if (!isarr(x)) { dprintf( ("making %s into an array\n", NN(x->nval)) ); if (freeable(x)) xfree(x->sval); x->tval &= ~(STR|NUM|DONTFREE); x->tval |= ARR; x->sval = (char *) makesymtab(NSYMTAB); } z = setsymtab(buf, "", 0.0, STR|NUM, (Array *) x->sval); z->ctype = OCELL; z->csub = CVAR; tempfree(x); free(buf); return(z); } Cell *awkdelete(Node **a, int n) /* a[0] is symtab, a[1] is list of subscripts */ { Cell *x, *y; Node *np; char *s; int nsub = strlen(*SUBSEP); x = execute(a[0]); /* Cell* for symbol table */ if (!isarr(x)) return True; if (a[1] == 0) { /* delete the elements, not the table */ freesymtab(x); x->tval &= ~STR; x->tval |= ARR; x->sval = (char *) makesymtab(NSYMTAB); } else { int bufsz = recsize; char *buf; if ((buf = (char *) malloc(bufsz)) == NULL) FATAL("out of memory in adelete"); buf[0] = 0; for (np = a[1]; np; np = np->nnext) { y = execute(np); /* subscript */ s = getsval(y); if (!adjbuf(&buf, &bufsz, strlen(buf)+strlen(s)+nsub+1, recsize, 0, "awkdelete")) FATAL("out of memory deleting %s[%s...]", x->nval, buf); strcat(buf, s); if (np->nnext) strcat(buf, *SUBSEP); tempfree(y); } freeelem(x, buf); free(buf); } tempfree(x); return True; } Cell *intest(Node **a, int n) /* a[0] is index (list), a[1] is symtab */ { Cell *x, *ap, *k; Node *p; char *buf; char *s; int bufsz = recsize; int nsub = strlen(*SUBSEP); ap = execute(a[1]); /* array name */ if (!isarr(ap)) { dprintf( ("making %s into an array\n", ap->nval) ); if (freeable(ap)) xfree(ap->sval); ap->tval &= ~(STR|NUM|DONTFREE); ap->tval |= ARR; ap->sval = (char *) makesymtab(NSYMTAB); } if ((buf = (char *) malloc(bufsz)) == NULL) { FATAL("out of memory in intest"); } buf[0] = 0; for (p = a[0]; p; p = p->nnext) { x = execute(p); /* expr */ s = getsval(x); if (!adjbuf(&buf, &bufsz, strlen(buf)+strlen(s)+nsub+1, recsize, 0, "intest")) FATAL("out of memory deleting %s[%s...]", x->nval, buf); strcat(buf, s); tempfree(x); if (p->nnext) strcat(buf, *SUBSEP); } k = lookup(buf, (Array *) ap->sval); tempfree(ap); free(buf); if (k == NULL) return(False); else return(True); } Cell *matchop(Node **a, int n) /* ~ and match() */ { Cell *x, *y; char *s, *t; int i; fa *pfa; int (*mf)(fa *, const char *) = match, mode = 0; if (n == MATCHFCN) { mf = pmatch; mode = 1; } x = execute(a[1]); /* a[1] = target text */ s = getsval(x); if (a[0] == 0) /* a[1] == 0: already-compiled reg expr */ i = (*mf)((fa *) a[2], s); else { y = execute(a[2]); /* a[2] = regular expr */ t = getsval(y); pfa = makedfa(t, mode); i = (*mf)(pfa, s); tempfree(y); } tempfree(x); if (n == MATCHFCN) { int start = patbeg - s + 1; if (patlen < 0) start = 0; setfval(rstartloc, (Awkfloat) start); setfval(rlengthloc, (Awkfloat) patlen); x = gettemp(); x->tval = NUM; x->fval = start; return x; } else if ((n == MATCH && i == 1) || (n == NOTMATCH && i == 0)) return(True); else return(False); } Cell *boolop(Node **a, int n) /* a[0] || a[1], a[0] && a[1], !a[0] */ { Cell *x, *y; int i; x = execute(a[0]); i = istrue(x); tempfree(x); switch (n) { case BOR: if (i) return(True); y = execute(a[1]); i = istrue(y); tempfree(y); if (i) return(True); else return(False); case AND: if ( !i ) return(False); y = execute(a[1]); i = istrue(y); tempfree(y); if (i) return(True); else return(False); case NOT: if (i) return(False); else return(True); default: /* can't happen */ FATAL("unknown boolean operator %d", n); } return 0; /*NOTREACHED*/ } Cell *relop(Node **a, int n) /* a[0 < a[1], etc. */ { int i; Cell *x, *y; Awkfloat j; x = execute(a[0]); y = execute(a[1]); if (x->tval&NUM && y->tval&NUM) { j = x->fval - y->fval; i = j<0? -1: (j>0? 1: 0); } else { i = strcmp(getsval(x), getsval(y)); } tempfree(x); tempfree(y); switch (n) { case LT: if (i<0) return(True); else return(False); case LE: if (i<=0) return(True); else return(False); case NE: if (i!=0) return(True); else return(False); case EQ: if (i == 0) return(True); else return(False); case GE: if (i>=0) return(True); else return(False); case GT: if (i>0) return(True); else return(False); default: /* can't happen */ FATAL("unknown relational operator %d", n); } return 0; /*NOTREACHED*/ } void tfree(Cell *a) /* free a tempcell */ { if (freeable(a)) { dprintf( ("freeing %s %s %o\n", NN(a->nval), NN(a->sval), a->tval) ); xfree(a->sval); } if (a == tmps) FATAL("tempcell list is curdled"); a->cnext = tmps; tmps = a; } Cell *gettemp(void) /* get a tempcell */ { int i; Cell *x; if (!tmps) { tmps = (Cell *) calloc(100, sizeof(Cell)); if (!tmps) FATAL("out of space for temporaries"); for(i = 1; i < 100; i++) tmps[i-1].cnext = &tmps[i]; tmps[i-1].cnext = 0; } x = tmps; tmps = x->cnext; *x = tempcell; return(x); } Cell *indirect(Node **a, int n) /* $( a[0] ) */ { Awkfloat val; Cell *x; int m; char *s; x = execute(a[0]); val = getfval(x); /* freebsd: defend against super large field numbers */ if ((Awkfloat)INT_MAX < val) FATAL("trying to access out of range field %s", x->nval); m = (int) val; if (m == 0 && !is_number(s = getsval(x))) /* suspicion! */ FATAL("illegal field $(%s), name \"%s\"", s, x->nval); /* BUG: can x->nval ever be null??? */ tempfree(x); x = fieldadr(m); x->ctype = OCELL; /* BUG? why are these needed? */ x->csub = CFLD; return(x); } Cell *substr(Node **a, int nnn) /* substr(a[0], a[1], a[2]) */ { int k, m, n; char *s; int temp; Cell *x, *y, *z = 0; x = execute(a[0]); y = execute(a[1]); if (a[2] != 0) z = execute(a[2]); s = getsval(x); k = strlen(s) + 1; if (k <= 1) { tempfree(x); tempfree(y); if (a[2] != 0) { tempfree(z); } x = gettemp(); setsval(x, ""); return(x); } m = (int) getfval(y); if (m <= 0) m = 1; else if (m > k) m = k; tempfree(y); if (a[2] != 0) { n = (int) getfval(z); tempfree(z); } else n = k - 1; if (n < 0) n = 0; else if (n > k - m) n = k - m; dprintf( ("substr: m=%d, n=%d, s=%s\n", m, n, s) ); y = gettemp(); temp = s[n+m-1]; /* with thanks to John Linderman */ s[n+m-1] = '\0'; setsval(y, s + m - 1); s[n+m-1] = temp; tempfree(x); return(y); } Cell *sindex(Node **a, int nnn) /* index(a[0], a[1]) */ { Cell *x, *y, *z; char *s1, *s2, *p1, *p2, *q; Awkfloat v = 0.0; x = execute(a[0]); s1 = getsval(x); y = execute(a[1]); s2 = getsval(y); z = gettemp(); for (p1 = s1; *p1 != '\0'; p1++) { for (q=p1, p2=s2; *p2 != '\0' && *q == *p2; q++, p2++) ; if (*p2 == '\0') { v = (Awkfloat) (p1 - s1 + 1); /* origin 1 */ break; } } tempfree(x); tempfree(y); setfval(z, v); return(z); } #define MAXNUMSIZE 50 int format(char **pbuf, int *pbufsize, const char *s, Node *a) /* printf-like conversions */ { char *fmt; char *p, *t; const char *os; Cell *x; int flag = 0, n; int fmtwd; /* format width */ int fmtsz = recsize; char *buf = *pbuf; int bufsize = *pbufsize; os = s; p = buf; if ((fmt = (char *) malloc(fmtsz)) == NULL) FATAL("out of memory in format()"); while (*s) { adjbuf(&buf, &bufsize, MAXNUMSIZE+1+p-buf, recsize, &p, "format1"); if (*s != '%') { *p++ = *s++; continue; } if (*(s+1) == '%') { *p++ = '%'; s += 2; continue; } /* have to be real careful in case this is a huge number, eg, %100000d */ fmtwd = atoi(s+1); if (fmtwd < 0) fmtwd = -fmtwd; adjbuf(&buf, &bufsize, fmtwd+1+p-buf, recsize, &p, "format2"); for (t = fmt; (*t++ = *s) != '\0'; s++) { if (!adjbuf(&fmt, &fmtsz, MAXNUMSIZE+1+t-fmt, recsize, &t, "format3")) FATAL("format item %.30s... ran format() out of memory", os); if (isalpha((uschar)*s) && *s != 'l' && *s != 'h' && *s != 'L') break; /* the ansi panoply */ if (*s == '*') { x = execute(a); a = a->nnext; sprintf(t-1, "%d", fmtwd=(int) getfval(x)); if (fmtwd < 0) fmtwd = -fmtwd; adjbuf(&buf, &bufsize, fmtwd+1+p-buf, recsize, &p, "format"); t = fmt + strlen(fmt); tempfree(x); } } *t = '\0'; if (fmtwd < 0) fmtwd = -fmtwd; adjbuf(&buf, &bufsize, fmtwd+1+p-buf, recsize, &p, "format4"); switch (*s) { case 'f': case 'e': case 'g': case 'E': case 'G': flag = 'f'; break; case 'd': case 'i': flag = 'd'; if(*(s-1) == 'l') break; *(t-1) = 'l'; *t = 'd'; *++t = '\0'; break; case 'o': case 'x': case 'X': case 'u': flag = *(s-1) == 'l' ? 'd' : 'u'; break; case 's': flag = 's'; break; case 'c': flag = 'c'; break; default: WARNING("weird printf conversion %s", fmt); flag = '?'; break; } if (a == NULL) FATAL("not enough args in printf(%s)", os); x = execute(a); a = a->nnext; n = MAXNUMSIZE; if (fmtwd > n) n = fmtwd; adjbuf(&buf, &bufsize, 1+n+p-buf, recsize, &p, "format5"); switch (flag) { case '?': sprintf(p, "%s", fmt); /* unknown, so dump it too */ t = getsval(x); n = strlen(t); if (fmtwd > n) n = fmtwd; adjbuf(&buf, &bufsize, 1+strlen(p)+n+p-buf, recsize, &p, "format6"); p += strlen(p); sprintf(p, "%s", t); break; case 'f': sprintf(p, fmt, getfval(x)); break; case 'd': sprintf(p, fmt, (long) getfval(x)); break; case 'u': sprintf(p, fmt, (int) getfval(x)); break; case 's': t = getsval(x); n = strlen(t); if (fmtwd > n) n = fmtwd; if (!adjbuf(&buf, &bufsize, 1+n+p-buf, recsize, &p, "format7")) FATAL("huge string/format (%d chars) in printf %.30s... ran format() out of memory", n, t); sprintf(p, fmt, t); break; case 'c': if (isnum(x)) { if (getfval(x)) sprintf(p, fmt, (int) getfval(x)); else { *p++ = '\0'; /* explicit null byte */ *p = '\0'; /* next output will start here */ } } else sprintf(p, fmt, getsval(x)[0]); break; default: FATAL("can't happen: bad conversion %c in format()", flag); } tempfree(x); p += strlen(p); s++; } *p = '\0'; free(fmt); for ( ; a; a = a->nnext) /* evaluate any remaining args */ execute(a); *pbuf = buf; *pbufsize = bufsize; return p - buf; } Cell *awksprintf(Node **a, int n) /* sprintf(a[0]) */ { Cell *x; Node *y; char *buf; int bufsz=3*recsize; if ((buf = (char *) malloc(bufsz)) == NULL) FATAL("out of memory in awksprintf"); y = a[0]->nnext; x = execute(a[0]); if (format(&buf, &bufsz, getsval(x), y) == -1) FATAL("sprintf string %.30s... too long. can't happen.", buf); tempfree(x); x = gettemp(); x->sval = buf; x->tval = STR; return(x); } Cell *awkprintf(Node **a, int n) /* printf */ { /* a[0] is list of args, starting with format string */ /* a[1] is redirection operator, a[2] is redirection file */ FILE *fp; Cell *x; Node *y; char *buf; int len; int bufsz=3*recsize; if ((buf = (char *) malloc(bufsz)) == NULL) FATAL("out of memory in awkprintf"); y = a[0]->nnext; x = execute(a[0]); if ((len = format(&buf, &bufsz, getsval(x), y)) == -1) FATAL("printf string %.30s... too long. can't happen.", buf); tempfree(x); if (a[1] == NULL) { /* fputs(buf, stdout); */ fwrite(buf, len, 1, stdout); if (ferror(stdout)) FATAL("write error on stdout"); } else { fp = redirect(ptoi(a[1]), a[2]); /* fputs(buf, fp); */ fwrite(buf, len, 1, fp); fflush(fp); if (ferror(fp)) FATAL("write error on %s", filename(fp)); } free(buf); return(True); } Cell *arith(Node **a, int n) /* a[0] + a[1], etc. also -a[0] */ { Awkfloat i, j = 0; double v; Cell *x, *y, *z; x = execute(a[0]); i = getfval(x); tempfree(x); if (n != UMINUS) { y = execute(a[1]); j = getfval(y); tempfree(y); } z = gettemp(); switch (n) { case ADD: i += j; break; case MINUS: i -= j; break; case MULT: i *= j; break; case DIVIDE: if (j == 0) FATAL("division by zero"); i /= j; break; case MOD: if (j == 0) FATAL("division by zero in mod"); modf(i/j, &v); i = i - j * v; break; case UMINUS: i = -i; break; case POWER: if (j >= 0 && modf(j, &v) == 0.0) /* pos integer exponent */ i = ipow(i, (int) j); else i = errcheck(pow(i, j), "pow"); break; default: /* can't happen */ FATAL("illegal arithmetic operator %d", n); } setfval(z, i); return(z); } double ipow(double x, int n) /* x**n. ought to be done by pow, but isn't always */ { double v; if (n <= 0) return 1; v = ipow(x, n/2); if (n % 2 == 0) return v * v; else return x * v * v; } Cell *incrdecr(Node **a, int n) /* a[0]++, etc. */ { Cell *x, *z; int k; Awkfloat xf; x = execute(a[0]); xf = getfval(x); k = (n == PREINCR || n == POSTINCR) ? 1 : -1; if (n == PREINCR || n == PREDECR) { setfval(x, xf + k); return(x); } z = gettemp(); setfval(z, xf); setfval(x, xf + k); tempfree(x); return(z); } Cell *assign(Node **a, int n) /* a[0] = a[1], a[0] += a[1], etc. */ { /* this is subtle; don't muck with it. */ Cell *x, *y; Awkfloat xf, yf; double v; y = execute(a[1]); x = execute(a[0]); if (n == ASSIGN) { /* ordinary assignment */ if (x == y && !(x->tval & (FLD|REC))) /* self-assignment: */ ; /* leave alone unless it's a field */ else if ((y->tval & (STR|NUM)) == (STR|NUM)) { setsval(x, getsval(y)); x->fval = getfval(y); x->tval |= NUM; } else if (isstr(y)) setsval(x, getsval(y)); else if (isnum(y)) setfval(x, getfval(y)); else funnyvar(y, "read value of"); tempfree(y); return(x); } xf = getfval(x); yf = getfval(y); switch (n) { case ADDEQ: xf += yf; break; case SUBEQ: xf -= yf; break; case MULTEQ: xf *= yf; break; case DIVEQ: if (yf == 0) FATAL("division by zero in /="); xf /= yf; break; case MODEQ: if (yf == 0) FATAL("division by zero in %%="); modf(xf/yf, &v); xf = xf - yf * v; break; case POWEQ: if (yf >= 0 && modf(yf, &v) == 0.0) /* pos integer exponent */ xf = ipow(xf, (int) yf); else xf = errcheck(pow(xf, yf), "pow"); break; default: FATAL("illegal assignment operator %d", n); break; } tempfree(y); setfval(x, xf); return(x); } Cell *cat(Node **a, int q) /* a[0] cat a[1] */ { Cell *x, *y, *z; int n1, n2; char *s; x = execute(a[0]); y = execute(a[1]); getsval(x); getsval(y); n1 = strlen(x->sval); n2 = strlen(y->sval); s = (char *) malloc(n1 + n2 + 1); if (s == NULL) FATAL("out of space concatenating %.15s... and %.15s...", x->sval, y->sval); strcpy(s, x->sval); strcpy(s+n1, y->sval); tempfree(x); tempfree(y); z = gettemp(); z->sval = s; z->tval = STR; return(z); } Cell *pastat(Node **a, int n) /* a[0] { a[1] } */ { Cell *x; if (a[0] == 0) x = execute(a[1]); else { x = execute(a[0]); if (istrue(x)) { tempfree(x); x = execute(a[1]); } } return x; } Cell *dopa2(Node **a, int n) /* a[0], a[1] { a[2] } */ { Cell *x; int pair; pair = ptoi(a[3]); if (pairstack[pair] == 0) { x = execute(a[0]); if (istrue(x)) pairstack[pair] = 1; tempfree(x); } if (pairstack[pair] == 1) { x = execute(a[1]); if (istrue(x)) pairstack[pair] = 0; tempfree(x); x = execute(a[2]); return(x); } return(False); } Cell *split(Node **a, int nnn) /* split(a[0], a[1], a[2]); a[3] is type */ { Cell *x = 0, *y, *ap; char *s; int sep; char *t, temp, num[50], *fs = 0; int n, tempstat, arg3type; y = execute(a[0]); /* source string */ s = getsval(y); arg3type = ptoi(a[3]); if (a[2] == 0) /* fs string */ fs = *FS; else if (arg3type == STRING) { /* split(str,arr,"string") */ x = execute(a[2]); fs = getsval(x); } else if (arg3type == REGEXPR) fs = "(regexpr)"; /* split(str,arr,/regexpr/) */ else FATAL("illegal type of split"); sep = *fs; ap = execute(a[1]); /* array name */ freesymtab(ap); dprintf( ("split: s=|%s|, a=%s, sep=|%s|\n", s, NN(ap->nval), fs) ); ap->tval &= ~STR; ap->tval |= ARR; ap->sval = (char *) makesymtab(NSYMTAB); n = 0; if (arg3type == REGEXPR && strlen((char*)((fa*)a[2])->restr) == 0) { /* split(s, a, //); have to arrange that it looks like empty sep */ arg3type = 0; fs = ""; sep = 0; } if (*s != '\0' && (strlen(fs) > 1 || arg3type == REGEXPR)) { /* reg expr */ fa *pfa; if (arg3type == REGEXPR) { /* it's ready already */ pfa = (fa *) a[2]; } else { pfa = makedfa(fs, 1); } if (nematch(pfa,s)) { tempstat = pfa->initstat; pfa->initstat = 2; do { n++; sprintf(num, "%d", n); temp = *patbeg; *patbeg = '\0'; if (is_number(s)) setsymtab(num, s, atof(s), STR|NUM, (Array *) ap->sval); else setsymtab(num, s, 0.0, STR, (Array *) ap->sval); *patbeg = temp; s = patbeg + patlen; if (*(patbeg+patlen-1) == 0 || *s == 0) { n++; sprintf(num, "%d", n); setsymtab(num, "", 0.0, STR, (Array *) ap->sval); pfa->initstat = tempstat; goto spdone; } } while (nematch(pfa,s)); pfa->initstat = tempstat; /* bwk: has to be here to reset */ /* cf gsub and refldbld */ } n++; sprintf(num, "%d", n); if (is_number(s)) setsymtab(num, s, atof(s), STR|NUM, (Array *) ap->sval); else setsymtab(num, s, 0.0, STR, (Array *) ap->sval); spdone: pfa = NULL; } else if (sep == ' ') { for (n = 0; ; ) { while (*s == ' ' || *s == '\t' || *s == '\n') s++; if (*s == 0) break; n++; t = s; do s++; while (*s!=' ' && *s!='\t' && *s!='\n' && *s!='\0'); temp = *s; *s = '\0'; sprintf(num, "%d", n); if (is_number(t)) setsymtab(num, t, atof(t), STR|NUM, (Array *) ap->sval); else setsymtab(num, t, 0.0, STR, (Array *) ap->sval); *s = temp; if (*s != 0) s++; } } else if (sep == 0) { /* new: split(s, a, "") => 1 char/elem */ for (n = 0; *s != 0; s++) { char buf[2]; n++; sprintf(num, "%d", n); buf[0] = *s; buf[1] = 0; if (isdigit((uschar)buf[0])) setsymtab(num, buf, atof(buf), STR|NUM, (Array *) ap->sval); else setsymtab(num, buf, 0.0, STR, (Array *) ap->sval); } } else if (*s != 0) { for (;;) { n++; t = s; while (*s != sep && *s != '\n' && *s != '\0') s++; temp = *s; *s = '\0'; sprintf(num, "%d", n); if (is_number(t)) setsymtab(num, t, atof(t), STR|NUM, (Array *) ap->sval); else setsymtab(num, t, 0.0, STR, (Array *) ap->sval); *s = temp; if (*s++ == 0) break; } } tempfree(ap); tempfree(y); if (a[2] != 0 && arg3type == STRING) { tempfree(x); } x = gettemp(); x->tval = NUM; x->fval = n; return(x); } Cell *condexpr(Node **a, int n) /* a[0] ? a[1] : a[2] */ { Cell *x; x = execute(a[0]); if (istrue(x)) { tempfree(x); x = execute(a[1]); } else { tempfree(x); x = execute(a[2]); } return(x); } Cell *ifstat(Node **a, int n) /* if (a[0]) a[1]; else a[2] */ { Cell *x; x = execute(a[0]); if (istrue(x)) { tempfree(x); x = execute(a[1]); } else if (a[2] != 0) { tempfree(x); x = execute(a[2]); } return(x); } Cell *whilestat(Node **a, int n) /* while (a[0]) a[1] */ { Cell *x; for (;;) { x = execute(a[0]); if (!istrue(x)) return(x); tempfree(x); x = execute(a[1]); if (isbreak(x)) { x = True; return(x); } if (isnext(x) || isexit(x) || isret(x)) return(x); tempfree(x); } } Cell *dostat(Node **a, int n) /* do a[0]; while(a[1]) */ { Cell *x; for (;;) { x = execute(a[0]); if (isbreak(x)) return True; if (isnext(x) || isexit(x) || isret(x)) return(x); tempfree(x); x = execute(a[1]); if (!istrue(x)) return(x); tempfree(x); } } Cell *forstat(Node **a, int n) /* for (a[0]; a[1]; a[2]) a[3] */ { Cell *x; x = execute(a[0]); tempfree(x); for (;;) { if (a[1]!=0) { x = execute(a[1]); if (!istrue(x)) return(x); else tempfree(x); } x = execute(a[3]); if (isbreak(x)) /* turn off break */ return True; if (isnext(x) || isexit(x) || isret(x)) return(x); tempfree(x); x = execute(a[2]); tempfree(x); } } Cell *instat(Node **a, int n) /* for (a[0] in a[1]) a[2] */ { Cell *x, *vp, *arrayp, *cp, *ncp; Array *tp; int i; vp = execute(a[0]); arrayp = execute(a[1]); if (!isarr(arrayp)) { return True; } tp = (Array *) arrayp->sval; tempfree(arrayp); for (i = 0; i < tp->size; i++) { /* this routine knows too much */ for (cp = tp->tab[i]; cp != NULL; cp = ncp) { setsval(vp, cp->nval); ncp = cp->cnext; x = execute(a[2]); if (isbreak(x)) { tempfree(vp); return True; } if (isnext(x) || isexit(x) || isret(x)) { tempfree(vp); return(x); } tempfree(x); } } return True; } Cell *bltin(Node **a, int n) /* builtin functions. a[0] is type, a[1] is arg list */ { Cell *x, *y; Awkfloat u; int t; Awkfloat tmp; char *p, *buf; Node *nextarg; FILE *fp; void flush_all(void); t = ptoi(a[0]); x = execute(a[1]); nextarg = a[1]->nnext; switch (t) { case FLENGTH: if (isarr(x)) u = ((Array *) x->sval)->nelem; /* GROT. should be function*/ else u = strlen(getsval(x)); break; case FLOG: u = errcheck(log(getfval(x)), "log"); break; case FINT: modf(getfval(x), &u); break; case FEXP: u = errcheck(exp(getfval(x)), "exp"); break; case FSQRT: u = errcheck(sqrt(getfval(x)), "sqrt"); break; case FSIN: u = sin(getfval(x)); break; case FCOS: u = cos(getfval(x)); break; case FATAN: if (nextarg == 0) { WARNING("atan2 requires two arguments; returning 1.0"); u = 1.0; } else { y = execute(a[1]->nnext); u = atan2(getfval(x), getfval(y)); tempfree(y); nextarg = nextarg->nnext; } break; case FSYSTEM: fflush(stdout); /* in case something is buffered already */ u = (Awkfloat) system(getsval(x)) / 256; /* 256 is unix-dep */ break; case FRAND: /* in principle, rand() returns something in 0..RAND_MAX */ u = (Awkfloat) (rand() % RAND_MAX) / RAND_MAX; break; case FSRAND: if (isrec(x)) /* no argument provided */ u = time((time_t *)0); else u = getfval(x); tmp = u; srand((unsigned int) u); u = srand_seed; srand_seed = tmp; break; case FTOUPPER: case FTOLOWER: buf = tostring(getsval(x)); if (t == FTOUPPER) { for (p = buf; *p; p++) if (islower((uschar) *p)) *p = toupper((uschar)*p); } else { for (p = buf; *p; p++) if (isupper((uschar) *p)) *p = tolower((uschar)*p); } tempfree(x); x = gettemp(); setsval(x, buf); free(buf); return x; case FFLUSH: if (isrec(x) || strlen(getsval(x)) == 0) { flush_all(); /* fflush() or fflush("") -> all */ u = 0; } else if ((fp = openfile(FFLUSH, getsval(x))) == NULL) u = EOF; else u = fflush(fp); break; default: /* can't happen */ if ((y = bio_func(t, x, a)) != 0) { tempfree(x); return y; } FATAL("illegal function type %d", t); break; } tempfree(x); x = gettemp(); setfval(x, u); if (nextarg != 0) { WARNING("warning: function has too many arguments"); for ( ; nextarg; nextarg = nextarg->nnext) execute(nextarg); } return(x); } Cell *printstat(Node **a, int n) /* print a[0] */ { Node *x; Cell *y; FILE *fp; if (a[1] == 0) /* a[1] is redirection operator, a[2] is file */ fp = stdout; else fp = redirect(ptoi(a[1]), a[2]); for (x = a[0]; x != NULL; x = x->nnext) { y = execute(x); fputs(getpssval(y), fp); tempfree(y); if (x->nnext == NULL) fputs(*ORS, fp); else fputs(*OFS, fp); } if (a[1] != 0) fflush(fp); if (ferror(fp)) FATAL("write error on %s", filename(fp)); return(True); } Cell *nullproc(Node **a, int n) { n = n; a = a; return 0; } FILE *redirect(int a, Node *b) /* set up all i/o redirections */ { FILE *fp; Cell *x; char *fname; x = execute(b); fname = getsval(x); fp = openfile(a, fname); if (fp == NULL) FATAL("can't open file %s", fname); tempfree(x); return fp; } struct files { FILE *fp; const char *fname; int mode; /* '|', 'a', 'w' => LE/LT, GT */ } *files; int nfiles; void stdinit(void) /* in case stdin, etc., are not constants */ { nfiles = FOPEN_MAX; files = calloc(nfiles, sizeof(*files)); if (files == NULL) FATAL("can't allocate file memory for %u files", nfiles); files[0].fp = stdin; files[0].fname = "/dev/stdin"; files[0].mode = LT; files[1].fp = stdout; files[1].fname = "/dev/stdout"; files[1].mode = GT; files[2].fp = stderr; files[2].fname = "/dev/stderr"; files[2].mode = GT; } FILE *openfile(int a, const char *us) { const char *s = us; int i, m; FILE *fp = 0; if (*s == '\0') FATAL("null file name in print or getline"); for (i=0; i < nfiles; i++) if (files[i].fname && strcmp(s, files[i].fname) == 0) { if (a == files[i].mode || (a==APPEND && files[i].mode==GT)) return files[i].fp; if (a == FFLUSH) return files[i].fp; } if (a == FFLUSH) /* didn't find it, so don't create it! */ return NULL; for (i=0; i < nfiles; i++) if (files[i].fp == 0) break; if (i >= nfiles) { struct files *nf; int nnf = nfiles + FOPEN_MAX; nf = realloc(files, nnf * sizeof(*nf)); if (nf == NULL) FATAL("cannot grow files for %s and %d files", s, nnf); memset(&nf[nfiles], 0, FOPEN_MAX * sizeof(*nf)); nfiles = nnf; files = nf; } fflush(stdout); /* force a semblance of order */ m = a; if (a == GT) { fp = fopen(s, "w"); } else if (a == APPEND) { fp = fopen(s, "a"); m = GT; /* so can mix > and >> */ } else if (a == '|') { /* output pipe */ fp = popen(s, "w"); } else if (a == LE) { /* input pipe */ fp = popen(s, "r"); } else if (a == LT) { /* getline sval, files[i].fname) == 0) { if (ferror(files[i].fp)) WARNING( "i/o error occurred on %s", files[i].fname ); if (files[i].mode == '|' || files[i].mode == LE) stat = pclose(files[i].fp); else stat = fclose(files[i].fp); if (stat == EOF) WARNING( "i/o error occurred closing %s", files[i].fname ); if (i > 2) /* don't do /dev/std... */ xfree(files[i].fname); files[i].fname = NULL; /* watch out for ref thru this */ files[i].fp = NULL; } } tempfree(x); x = gettemp(); setfval(x, (Awkfloat) stat); return(x); } void closeall(void) { int i, stat; for (i = 0; i < FOPEN_MAX; i++) { if (files[i].fp) { if (ferror(files[i].fp)) WARNING( "i/o error occurred on %s", files[i].fname ); if (files[i].mode == '|' || files[i].mode == LE) stat = pclose(files[i].fp); else stat = fclose(files[i].fp); if (stat == EOF) WARNING( "i/o error occurred while closing %s", files[i].fname ); } } } void flush_all(void) { int i; for (i = 0; i < nfiles; i++) if (files[i].fp) fflush(files[i].fp); } void backsub(char **pb_ptr, char **sptr_ptr); Cell *sub(Node **a, int nnn) /* substitute command */ { char *sptr, *pb, *q; Cell *x, *y, *result; char *t, *buf; fa *pfa; int bufsz = recsize; if ((buf = (char *) malloc(bufsz)) == NULL) FATAL("out of memory in sub"); x = execute(a[3]); /* target string */ t = getsval(x); if (a[0] == 0) /* 0 => a[1] is already-compiled regexpr */ pfa = (fa *) a[1]; /* regular expression */ else { y = execute(a[1]); pfa = makedfa(getsval(y), 1); tempfree(y); } y = execute(a[2]); /* replacement string */ result = False; if (pmatch(pfa, t)) { sptr = t; adjbuf(&buf, &bufsz, 1+patbeg-sptr, recsize, 0, "sub"); pb = buf; while (sptr < patbeg) *pb++ = *sptr++; sptr = getsval(y); while (*sptr != 0) { adjbuf(&buf, &bufsz, 5+pb-buf, recsize, &pb, "sub"); if (*sptr == '\\') { backsub(&pb, &sptr); } else if (*sptr == '&') { sptr++; adjbuf(&buf, &bufsz, 1+patlen+pb-buf, recsize, &pb, "sub"); for (q = patbeg; q < patbeg+patlen; ) *pb++ = *q++; } else *pb++ = *sptr++; } *pb = '\0'; if (pb > buf + bufsz) FATAL("sub result1 %.30s too big; can't happen", buf); sptr = patbeg + patlen; if ((patlen == 0 && *patbeg) || (patlen && *(sptr-1))) { adjbuf(&buf, &bufsz, 1+strlen(sptr)+pb-buf, 0, &pb, "sub"); while ((*pb++ = *sptr++) != 0) ; } if (pb > buf + bufsz) FATAL("sub result2 %.30s too big; can't happen", buf); setsval(x, buf); /* BUG: should be able to avoid copy */ result = True;; } tempfree(x); tempfree(y); free(buf); return result; } Cell *gsub(Node **a, int nnn) /* global substitute */ { Cell *x, *y; char *rptr, *sptr, *t, *pb, *q; char *buf; fa *pfa; int mflag, tempstat, num; int bufsz = recsize; if ((buf = (char *) malloc(bufsz)) == NULL) FATAL("out of memory in gsub"); mflag = 0; /* if mflag == 0, can replace empty string */ num = 0; x = execute(a[3]); /* target string */ t = getsval(x); if (a[0] == 0) /* 0 => a[1] is already-compiled regexpr */ pfa = (fa *) a[1]; /* regular expression */ else { y = execute(a[1]); pfa = makedfa(getsval(y), 1); tempfree(y); } y = execute(a[2]); /* replacement string */ if (pmatch(pfa, t)) { tempstat = pfa->initstat; pfa->initstat = 2; pb = buf; rptr = getsval(y); do { if (patlen == 0 && *patbeg != 0) { /* matched empty string */ if (mflag == 0) { /* can replace empty */ num++; sptr = rptr; while (*sptr != 0) { adjbuf(&buf, &bufsz, 5+pb-buf, recsize, &pb, "gsub"); if (*sptr == '\\') { backsub(&pb, &sptr); } else if (*sptr == '&') { sptr++; adjbuf(&buf, &bufsz, 1+patlen+pb-buf, recsize, &pb, "gsub"); for (q = patbeg; q < patbeg+patlen; ) *pb++ = *q++; } else *pb++ = *sptr++; } } if (*t == 0) /* at end */ goto done; adjbuf(&buf, &bufsz, 2+pb-buf, recsize, &pb, "gsub"); *pb++ = *t++; if (pb > buf + bufsz) /* BUG: not sure of this test */ FATAL("gsub result0 %.30s too big; can't happen", buf); mflag = 0; } else { /* matched nonempty string */ num++; sptr = t; adjbuf(&buf, &bufsz, 1+(patbeg-sptr)+pb-buf, recsize, &pb, "gsub"); while (sptr < patbeg) *pb++ = *sptr++; sptr = rptr; while (*sptr != 0) { adjbuf(&buf, &bufsz, 5+pb-buf, recsize, &pb, "gsub"); if (*sptr == '\\') { backsub(&pb, &sptr); } else if (*sptr == '&') { sptr++; adjbuf(&buf, &bufsz, 1+patlen+pb-buf, recsize, &pb, "gsub"); for (q = patbeg; q < patbeg+patlen; ) *pb++ = *q++; } else *pb++ = *sptr++; } t = patbeg + patlen; if (patlen == 0 || *t == 0 || *(t-1) == 0) goto done; if (pb > buf + bufsz) FATAL("gsub result1 %.30s too big; can't happen", buf); mflag = 1; } } while (pmatch(pfa,t)); sptr = t; adjbuf(&buf, &bufsz, 1+strlen(sptr)+pb-buf, 0, &pb, "gsub"); while ((*pb++ = *sptr++) != 0) ; done: if (pb < buf + bufsz) *pb = '\0'; else if (*(pb-1) != '\0') FATAL("gsub result2 %.30s truncated; can't happen", buf); setsval(x, buf); /* BUG: should be able to avoid copy + free */ pfa->initstat = tempstat; } tempfree(x); tempfree(y); x = gettemp(); x->tval = NUM; x->fval = num; free(buf); return(x); } void backsub(char **pb_ptr, char **sptr_ptr) /* handle \\& variations */ { /* sptr[0] == '\\' */ char *pb = *pb_ptr, *sptr = *sptr_ptr; if (sptr[1] == '\\') { if (sptr[2] == '\\' && sptr[3] == '&') { /* \\\& -> \& */ *pb++ = '\\'; *pb++ = '&'; sptr += 4; } else if (sptr[2] == '&') { /* \\& -> \ + matched */ *pb++ = '\\'; sptr += 2; } else { /* \\x -> \\x */ *pb++ = *sptr++; *pb++ = *sptr++; } } else if (sptr[1] == '&') { /* literal & */ sptr++; *pb++ = *sptr++; } else /* literal \ */ *pb++ = *sptr++; *pb_ptr = pb; *sptr_ptr = sptr; } bioawk-1.0/tran.c000066400000000000000000000304541220715177100137470ustar00rootroot00000000000000/**************************************************************** Copyright (C) Lucent Technologies 1997 All Rights Reserved Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that the copyright notice and this permission notice and warranty disclaimer appear in supporting documentation, and that the name Lucent Technologies or any of its entities not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ****************************************************************/ #define DEBUG #include #include #include #include #include #include "awk.h" #include "ytab.h" #define FULLTAB 2 /* rehash when table gets this x full */ #define GROWTAB 4 /* grow table by this factor */ Array *symtab; /* main symbol table */ char **FS; /* initial field sep */ char **RS; /* initial record sep */ char **OFS; /* output field sep */ char **ORS; /* output record sep */ char **OFMT; /* output format for numbers */ char **CONVFMT; /* format for conversions in getsval */ Awkfloat *NF; /* number of fields in current record */ Awkfloat *NR; /* number of current record */ Awkfloat *FNR; /* number of current record in current file */ char **FILENAME; /* current filename argument */ Awkfloat *ARGC; /* number of arguments from command line */ char **SUBSEP; /* subscript separator for a[i,j,k]; default \034 */ Awkfloat *RSTART; /* start of re matched with ~; origin 1 (!) */ Awkfloat *RLENGTH; /* length of same */ Cell *fsloc; /* FS */ Cell *nrloc; /* NR */ Cell *nfloc; /* NF */ Cell *fnrloc; /* FNR */ Array *ARGVtab; /* symbol table containing ARGV[...] */ Array *ENVtab; /* symbol table containing ENVIRON[...] */ Cell *rstartloc; /* RSTART */ Cell *rlengthloc; /* RLENGTH */ Cell *symtabloc; /* SYMTAB */ Cell *nullloc; /* a guaranteed empty cell */ Node *nullnode; /* zero&null, converted into a node for comparisons */ Cell *literal0; extern Cell **fldtab; void syminit(void) /* initialize symbol table with builtin vars */ { literal0 = setsymtab("0", "0", 0.0, NUM|STR|CON|DONTFREE, symtab); /* this is used for if(x)... tests: */ nullloc = setsymtab("$zero&null", "", 0.0, NUM|STR|CON|DONTFREE, symtab); nullnode = celltonode(nullloc, CCON); fsloc = setsymtab("FS", DEFAULT_FS, 0.0, STR|DONTFREE, symtab); FS = &fsloc->sval; RS = &setsymtab("RS", "\n", 0.0, STR|DONTFREE, symtab)->sval; OFS = &setsymtab("OFS", DEFAULT_FS, 0.0, STR|DONTFREE, symtab)->sval; ORS = &setsymtab("ORS", "\n", 0.0, STR|DONTFREE, symtab)->sval; OFMT = &setsymtab("OFMT", "%.6g", 0.0, STR|DONTFREE, symtab)->sval; CONVFMT = &setsymtab("CONVFMT", "%.6g", 0.0, STR|DONTFREE, symtab)->sval; FILENAME = &setsymtab("FILENAME", "", 0.0, STR|DONTFREE, symtab)->sval; nfloc = setsymtab("NF", "", 0.0, NUM, symtab); NF = &nfloc->fval; nrloc = setsymtab("NR", "", 0.0, NUM, symtab); NR = &nrloc->fval; fnrloc = setsymtab("FNR", "", 0.0, NUM, symtab); FNR = &fnrloc->fval; SUBSEP = &setsymtab("SUBSEP", "\034", 0.0, STR|DONTFREE, symtab)->sval; rstartloc = setsymtab("RSTART", "", 0.0, NUM, symtab); RSTART = &rstartloc->fval; rlengthloc = setsymtab("RLENGTH", "", 0.0, NUM, symtab); RLENGTH = &rlengthloc->fval; symtabloc = setsymtab("SYMTAB", "", 0.0, ARR, symtab); symtabloc->sval = (char *) symtab; } void arginit(int ac, char **av) /* set up ARGV and ARGC */ { Cell *cp; int i; char temp[50]; ARGC = &setsymtab("ARGC", "", (Awkfloat) ac, NUM, symtab)->fval; cp = setsymtab("ARGV", "", 0.0, ARR, symtab); ARGVtab = makesymtab(NSYMTAB); /* could be (int) ARGC as well */ cp->sval = (char *) ARGVtab; for (i = 0; i < ac; i++) { sprintf(temp, "%d", i); if (is_number(*av)) setsymtab(temp, *av, atof(*av), STR|NUM, ARGVtab); else setsymtab(temp, *av, 0.0, STR, ARGVtab); av++; } } void envinit(char **envp) /* set up ENVIRON variable */ { Cell *cp; char *p; cp = setsymtab("ENVIRON", "", 0.0, ARR, symtab); ENVtab = makesymtab(NSYMTAB); cp->sval = (char *) ENVtab; for ( ; *envp; envp++) { if ((p = strchr(*envp, '=')) == NULL) continue; if( p == *envp ) /* no left hand side name in env string */ continue; *p++ = 0; /* split into two strings at = */ if (is_number(p)) setsymtab(*envp, p, atof(p), STR|NUM, ENVtab); else setsymtab(*envp, p, 0.0, STR, ENVtab); p[-1] = '='; /* restore in case env is passed down to a shell */ } } Array *makesymtab(int n) /* make a new symbol table */ { Array *ap; Cell **tp; ap = (Array *) malloc(sizeof(Array)); tp = (Cell **) calloc(n, sizeof(Cell *)); if (ap == NULL || tp == NULL) FATAL("out of space in makesymtab"); ap->nelem = 0; ap->size = n; ap->tab = tp; return(ap); } void freesymtab(Cell *ap) /* free a symbol table */ { Cell *cp, *temp; Array *tp; int i; if (!isarr(ap)) return; tp = (Array *) ap->sval; if (tp == NULL) return; for (i = 0; i < tp->size; i++) { for (cp = tp->tab[i]; cp != NULL; cp = temp) { xfree(cp->nval); if (freeable(cp)) xfree(cp->sval); temp = cp->cnext; /* avoids freeing then using */ free(cp); tp->nelem--; } tp->tab[i] = 0; } if (tp->nelem != 0) WARNING("can't happen: inconsistent element count freeing %s", ap->nval); free(tp->tab); free(tp); } void freeelem(Cell *ap, const char *s) /* free elem s from ap (i.e., ap["s"] */ { Array *tp; Cell *p, *prev = NULL; int h; tp = (Array *) ap->sval; h = hash(s, tp->size); for (p = tp->tab[h]; p != NULL; prev = p, p = p->cnext) if (strcmp(s, p->nval) == 0) { if (prev == NULL) /* 1st one */ tp->tab[h] = p->cnext; else /* middle somewhere */ prev->cnext = p->cnext; if (freeable(p)) xfree(p->sval); free(p->nval); free(p); tp->nelem--; return; } } Cell *setsymtab(const char *n, const char *s, Awkfloat f, unsigned t, Array *tp) { int h; Cell *p; if (n != NULL && (p = lookup(n, tp)) != NULL) { dprintf( ("setsymtab found %p: n=%s s=\"%s\" f=%g t=%o\n", (void*)p, NN(p->nval), NN(p->sval), p->fval, p->tval) ); return(p); } p = (Cell *) malloc(sizeof(Cell)); if (p == NULL) FATAL("out of space for symbol table at %s", n); p->nval = tostring(n); p->sval = s ? tostring(s) : tostring(""); p->fval = f; p->tval = t; p->csub = CUNK; p->ctype = OCELL; tp->nelem++; if (tp->nelem > FULLTAB * tp->size) rehash(tp); h = hash(n, tp->size); p->cnext = tp->tab[h]; tp->tab[h] = p; dprintf( ("setsymtab set %p: n=%s s=\"%s\" f=%g t=%o\n", (void*)p, p->nval, p->sval, p->fval, p->tval) ); return(p); } int hash(const char *s, int n) /* form hash value for string s */ { unsigned hashval; for (hashval = 0; *s != '\0'; s++) hashval = (*s + 31 * hashval); return hashval % n; } void rehash(Array *tp) /* rehash items in small table into big one */ { int i, nh, nsz; Cell *cp, *op, **np; nsz = GROWTAB * tp->size; np = (Cell **) calloc(nsz, sizeof(Cell *)); if (np == NULL) /* can't do it, but can keep running. */ return; /* someone else will run out later. */ for (i = 0; i < tp->size; i++) { for (cp = tp->tab[i]; cp; cp = op) { op = cp->cnext; nh = hash(cp->nval, nsz); cp->cnext = np[nh]; np[nh] = cp; } } free(tp->tab); tp->tab = np; tp->size = nsz; } Cell *lookup(const char *s, Array *tp) /* look for s in tp */ { Cell *p; int h; h = hash(s, tp->size); for (p = tp->tab[h]; p != NULL; p = p->cnext) if (strcmp(s, p->nval) == 0) return(p); /* found it */ return(NULL); /* not found */ } Awkfloat setfval(Cell *vp, Awkfloat f) /* set float val of a Cell */ { int fldno; if ((vp->tval & (NUM | STR)) == 0) funnyvar(vp, "assign to"); if (isfld(vp)) { donerec = 0; /* mark $0 invalid */ fldno = atoi(vp->nval); if (fldno > *NF) newfld(fldno); dprintf( ("setting field %d to %g\n", fldno, f) ); } else if (isrec(vp)) { donefld = 0; /* mark $1... invalid */ donerec = 1; } if (freeable(vp)) xfree(vp->sval); /* free any previous string */ vp->tval &= ~STR; /* mark string invalid */ vp->tval |= NUM; /* mark number ok */ dprintf( ("setfval %p: %s = %g, t=%o\n", (void*)vp, NN(vp->nval), f, vp->tval) ); return vp->fval = f; } void funnyvar(Cell *vp, const char *rw) { if (isarr(vp)) FATAL("can't %s %s; it's an array name.", rw, vp->nval); if (vp->tval & FCN) FATAL("can't %s %s; it's a function.", rw, vp->nval); WARNING("funny variable %p: n=%s s=\"%s\" f=%g t=%o", vp, vp->nval, vp->sval, vp->fval, vp->tval); } char *setsval(Cell *vp, const char *s) /* set string val of a Cell */ { char *t; int fldno; dprintf( ("starting setsval %p: %s = \"%s\", t=%o, r,f=%d,%d\n", (void*)vp, NN(vp->nval), s, vp->tval, donerec, donefld) ); if ((vp->tval & (NUM | STR)) == 0) funnyvar(vp, "assign to"); if (isfld(vp)) { donerec = 0; /* mark $0 invalid */ fldno = atoi(vp->nval); if (fldno > *NF) newfld(fldno); dprintf( ("setting field %d to %s (%p)\n", fldno, s, s) ); } else if (isrec(vp)) { donefld = 0; /* mark $1... invalid */ donerec = 1; } t = tostring(s); /* in case it's self-assign */ if (freeable(vp)) xfree(vp->sval); vp->tval &= ~NUM; vp->tval |= STR; vp->tval &= ~DONTFREE; dprintf( ("setsval %p: %s = \"%s (%p) \", t=%o r,f=%d,%d\n", (void*)vp, NN(vp->nval), t,t, vp->tval, donerec, donefld) ); return(vp->sval = t); } Awkfloat getfval(Cell *vp) /* get float val of a Cell */ { if ((vp->tval & (NUM | STR)) == 0) funnyvar(vp, "read value of"); if (isfld(vp) && donefld == 0) fldbld(); else if (isrec(vp) && donerec == 0) recbld(); if (!isnum(vp)) { /* not a number */ vp->fval = atof(vp->sval); /* best guess */ if (is_number(vp->sval) && !(vp->tval&CON)) vp->tval |= NUM; /* make NUM only sparingly */ } dprintf( ("getfval %p: %s = %g, t=%o\n", (void*)vp, NN(vp->nval), vp->fval, vp->tval) ); return(vp->fval); } static char *get_str_val(Cell *vp, char **fmt) /* get string val of a Cell */ { char s[100]; /* BUG: unchecked */ double dtemp; if ((vp->tval & (NUM | STR)) == 0) funnyvar(vp, "read value of"); if (isfld(vp) && donefld == 0) fldbld(); else if (isrec(vp) && donerec == 0) recbld(); if (isstr(vp) == 0) { if (freeable(vp)) xfree(vp->sval); if (modf(vp->fval, &dtemp) == 0) /* it's integral */ sprintf(s, "%.30g", vp->fval); else sprintf(s, *fmt, vp->fval); vp->sval = tostring(s); vp->tval &= ~DONTFREE; vp->tval |= STR; } dprintf( ("getsval %p: %s = \"%s (%p)\", t=%o\n", (void*)vp, NN(vp->nval), vp->sval, vp->sval, vp->tval) ); return(vp->sval); } char *getsval(Cell *vp) /* get string val of a Cell */ { return get_str_val(vp, CONVFMT); } char *getpssval(Cell *vp) /* get string val of a Cell for print */ { return get_str_val(vp, OFMT); } char *tostring(const char *s) /* make a copy of string s */ { char *p; p = (char *) malloc(strlen(s)+1); if (p == NULL) FATAL("out of space in tostring on %s", s); strcpy(p, s); return(p); } char *qstring(const char *is, int delim) /* collect string up to next delim */ { const char *os = is; int c, n; uschar *s = (uschar *) is; uschar *buf, *bp; if ((buf = (uschar *) malloc(strlen(is)+3)) == NULL) FATAL( "out of space in qstring(%s)", s); for (bp = buf; (c = *s) != delim; s++) { if (c == '\n') SYNTAX( "newline in string %.20s...", os ); else if (c != '\\') *bp++ = c; else { /* \something */ c = *++s; if (c == 0) { /* \ at end */ *bp++ = '\\'; break; /* for loop */ } switch (c) { case '\\': *bp++ = '\\'; break; case 'n': *bp++ = '\n'; break; case 't': *bp++ = '\t'; break; case 'b': *bp++ = '\b'; break; case 'f': *bp++ = '\f'; break; case 'r': *bp++ = '\r'; break; default: if (!isdigit(c)) { *bp++ = c; break; } n = c - '0'; if (isdigit(s[1])) { n = 8 * n + *++s - '0'; if (isdigit(s[1])) n = 8 * n + *++s - '0'; } *bp++ = n; break; } } } *bp++ = 0; return (char *) buf; }