sra_sdk-2.1.7/0000775001221300116200000000000011647105277012647 5ustar rodarmertracesra_sdk-2.1.7/CHANGES0000664001221300116200000000261511645103617013640 0ustar rodarmertrace# =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== The NCBI SRA Software Development Kit Contact: sra-tools@ncbi.nlm.nih.gov Release documentation is now being delivered at http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software sra_sdk-2.1.7/Makefile0000644001221300116200000000677211627507532014317 0ustar rodarmertrace# =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== #------------------------------------------------------------------------------- # environment # TOP ?= $(CURDIR) include $(TOP)/build/Makefile.shell #------------------------------------------------------------------------------- # default # SUBDIRS = \ libs \ tools default: $(SUBDIRS) test: $(SUBDIRS) $(SUBDIRS) test: @ $(MAKE) -C $@ .PHONY: default $(SUBDIRS) test #------------------------------------------------------------------------------- # static vs. dynamic # static: @ touch "$(CURDIR)/build/STATIC" dynamic: @ rm -f "$(CURDIR)/build/STATIC" .PHONY: static dynamic #------------------------------------------------------------------------------- # all # SUBDIRS_ALL = $(addsuffix _all,$(SUBDIRS)) all: $(SUBDIRS_ALL) $(SUBDIRS_ALL): @ $(MAKE) -C $(subst _all,,$@) all .PHONY: all $(SUBDIRS_ALL) #------------------------------------------------------------------------------- # std # SUBDIRS_STD = $(addsuffix _std,$(SUBDIRS)) std: $(SUBDIRS_STD) $(SUBDIRS_STD): @ $(MAKE) -C $(subst _std,,$@) std .PHONY: std $(SUBDIRS_STD) #------------------------------------------------------------------------------- # clean # SUBDIRS_CLEAN = $(addsuffix _clean,$(SUBDIRS_ALL)) clean: $(SUBDIRS_CLEAN) $(SUBDIRS_CLEAN): @ $(MAKE) -C $(subst _all_clean,,$@) clean .PHONY: clean $(SUBDIRS_CLEAN) #------------------------------------------------------------------------------- # pass-through targets # COMPILERS = GCC ICC VC++ ARCHITECTURES = i386 x86_64 CONFIG = debug profile release PASSTHRUS = \ out bindir \ CC $(COMPILERS) \ $(ARCHITECTURES) \ $(CONFIG) $(PASSTHRUS): @ $(MAKE) TOP=$(CURDIR) -f build/Makefile.env $@ .PHONY: $(PASSTHRUS) #------------------------------------------------------------------------------- # configuration help # help configure: @ echo "Before initial build, run 'make OUTDIR= out' from" @ echo "the project root to set the output directory of your builds." @ echo @ echo "To select a compiler, run 'make ' where" @ echo "comp = { "$(COMPILERS)" }." @ echo @ echo "For hosts that support cross-compilation ( only Macintosh today )," @ echo "you can run 'make ' where arch = { "$(ARCHITECTURES)" }." @ echo @ echo "To set a build configuration, run 'make ' where" @ echo "config = { "$(CONFIG)" }." @ echo .PHONY: help configure sra_sdk-2.1.7/README0000664001221300116200000000522411632420742013521 0ustar rodarmertrace# =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== The NCBI SRA ( Sequence Read Archive ) Contact: sra-tools@ncbi.nlm.nih.gov http://trace.ncbi.nlm.nih.gov/Traces/sra/std The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. With this release, NCBI has implemented Compression by Reference, a sequence alignment compression process for storing sequence data. Currently BAM, Complete Genomics and Illumina export.txt formats contain alignment information. Compression by Reference only stores the difference in base pairs between sequence data and the segments it aligns to. The decompression process to restore original data such as fastq-dump would require fast access to the actual sequences of the references. NCBI recommends that SRA users dedicate local disk space to store local references downloaded from the NCBI SRA site. Linked references should be in a location accessible by the SRA Reader software. Older files in the NCBI system may not have been compressed using Compression by Reference. For more information on how to use Reference-based compressed files, download local references, and use related tools please refer to Compression by Reference file on the NCBI SRA website: "http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=softwareReadme" For additional information on using and building the toolkit, please visit our web site at: "http://trace.ncbi.nlm.nih.gov/Traces/sra/std" SRA Toolkit Development Team sra_sdk-2.1.7/USAGE0000644001221300116200000001567111645370373013445 0ustar rodarmertrace# =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== The NCBI SRA ( Sequence Read Archive ) Toolkit Contact: sra-tools@ncbi.nlm.nih.gov http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software For preliminary documentation on tool usage, consult the files within the "help" directory. CHANGES: SRA Toolkit includes new features in sam-dump tool and vdb-dump tools. Sam-dump now supports slicing across multiple sequences, and dumping cSRA files to fasta and fastq formats. In addition, sam-dump has three new parameters -=|--hide-identical Output '=' if base is identical to reference --gzip Compress output using gzip --bzip2 Compress output using bzip2 vdb-dump has two new parameters -o|--column_enum_short enumerates columns in short form -b|--boolean defines how boolean's are printed (1,T) We have combined the functionality of two scripts, config-assistant.perl and reference-assistant.perl into a single script, configuration-assistant.perl that helps users download the correct references for a given cSRA file and configure the user environment for the SRA Toolkit. DESCRIPTION: This release includes tools for reading the SRA archive, generally by converting individual runs into some commonly used format such as fastq. Support for NCBI's Compression by Reference is also included. "Linux" binaries have been created on CentOS and SuSE Linux distributions. They are not guaranteed to work on other distributions. In particular, the version of libc.so should be compatible. They are specific to the x86-family architectures. "Windows" binaries have been created using MSVC's (not Cygwin) tools. This release includes Win32 binaries. The "*-load" tools are not released for "Windows". "Mac OS X" binaries are available for the x86-family architectures. They will NOT run on PPC Macs. The 64-bit binaries will run only on OS 10.6. The 32-bit binaries should run on either 10.5 or later. CONTENTS: "abi-dump" - dump ABI color-space runs into their native format "abi-load" - load ABI color-space runs "fastq-dump" - dump any run of any platform in FASTQ format "fastq-load" - load FASTQ runs "helicos-load" - load HELICOS runs "illumina-dump" - dump Illumina runs into their native format "illumina-load" - load Illumina native runs "kar" - an archive extraction tool for .sra files "kdbmeta" - display the contents of one or more metadata stores "rcexplain" - print out error string for return codes (RC) "refseq-load" - ( NEW for Linux and Mac ) download a reference sequence object "sff-dump" - dump 454 runs into SFF format "sff-load" - load 454 SFF runs "sra-dbcc" - check SRA runs "sra-dump" - dump any run in a textual format [see note below] "sra-kar" - creates a single file archive from an SRA run "sra-stat" - display run column statistics "srf-load" - load SRF runs "sam-dump" - dump a cSRA into the SAM-format "vdb-copy" - copy SRA objects "vdb-dump" - display SRA objects in a textual format [see note below] "vdb-lock" - lock an object against modification "vdb-unlock" - unlock an object "align-info" - displays which references a csra-archive uses "vdb-config" - displays the configuration NOTES: The "sam-dump" tool only works on cSRA's. ( See README-csra ) The textual dumpers "sra-dump" and "vdb-dump" are provided in this release as an aid in visual inspection. It is likely that their actual output formatting will be changed in the near future to a stricter, more formalized representation[s]. The "help" information will be improved in near future releases, and the tool options will become standardized across the set. We will also be providing documentation on our web site. Tool options may change in the next release. Version 1 tool options will remain supported wherever possible in order to preserve operation of any existing scripts. CAVEATS: SRA tools are designed to handle very large amounts of data, and are not currently oriented toward desktop use. They work well within any Unix-like environment, such as Linux or MacOS's BSD shell. Windows operation presents a few challenges. We have tested our binaries under the MS "cmd.exe" shell and Cygwin's bash. Our tools know how to accept paths in Windows, Cygwin, POSIX and MinGW formats. Internally, all paths are treated as MinGW-style POSIX paths, so any information appearing in output will reflect this conversion: # simple file names SRR012345.sra => [NO CHANGE] # relative paths win\SRR012345.sra => win/SRR012345.sra # full or drive-relative paths C:\sra\win\SRR012345.sra => /C/sra/win/SRR012345.sra # network paths \\server\sra\SRR012345.sra => //server/sra/SRR012345.sra # POSIX paths /sra/posix/SRR012345.sra => [NO CHANGE] # Cygwin full paths /cygdrive/C/sra/SRR012345.sra => /C/sra/SRR012345.sra There are some situations where the software may behave unexpectedly due to path conversions. In particular, since Windows does not conform to POSIX path conventions, there may be difficulties combining network paths with non-network paths, explicitly or implicitly. IF YOU HAVE PROBLEMS, we recommend mounting file servers as network drives. If you run the software under Cygwin, you should take care to use either relative paths (those that do not begin with '/') or full paths that start with "/cygdrive/". The reason is that Cygwin provides its own path manipulation, but our tools are not aware of which shell they are running under. sra_sdk-2.1.7/build/0000775001221300116200000000000011630164537013742 5ustar rodarmertracesra_sdk-2.1.7/build/Makefile.env0000644001221300116200000001654011627507615016201 0ustar rodarmertrace# =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # pick up dependencies from object directory ifdef SRCDIR include $(wildcard *.d) endif # determine shell environment include $(TOP)/build/Makefile.shell # normally build shared and static external libs LIBEXT = $(LIBX) $(SHLX) # normally build static intermediate libs ILIBEXT = $(LIBX) # only build dynamic library modules MODEXT = $(SHLX) # determine BUILD ifeq (,$(BUILD)) BUILD = dbg endif # some rules are sensitive to the type of build BUILDTYPE = $(BUILD) # adjust settings for build ifeq (dbg,$(BUILD)) DEBUG := -D_DEBUGGING # ILIBEXT = $(LIBX) $(SHLX) MODEXT = $(LIBX) $(SHLX) endif ifeq (rel,$(BUILD)) DEBUG := -DNDEBUG endif ifeq (prof,$(BUILD)) DEBUG := -DNDEBUG -D_PROFILING STATIC = --static endif ifeq (pub,$(BUILD)) DEBUG := -DNDEBUG BUILDTYPE = rel STATIC = --static STATICSYSLIBS := --static-system-libs endif # allow for an all-static build ifndef STATIC STATIC = $(shell test -f $(TOP)/build/STATIC && echo "--static") endif ifeq (--static,$(STATIC)) LINKAGE := -D_STATIC LIBEXT = $(LIBX) ILIBEXT = $(LIBX) MODEXT = $(LIBX) endif # drop all suffix rules .SUFFIXES: # load OS and COMP specific files include $(TOP)/build/Makefile.$(OS) include $(TOP)/build/Makefile.$(COMP) include $(TOP)/build/Makefile.rules # full directory paths TARGDIR = $(OUTDIR)/$(OSFLAV)/$(BUILD)/$(COMP)/$(ARCH) BINDIR = $(TARGDIR)/bin ILIBDIR = $(TARGDIR)/ilib LIBDIR = $(TARGDIR)/lib MODDIR = $(TARGDIR)/mod WMODDIR = $(TARGDIR)/wmod OBJDIR = $(TARGDIR)/obj/$(MODULE) # path to the ncbi sub-directory # this is where modules and installed schema files are kept ifeq (win,$(OS)) # under Windows, we are always relative to binary path NCBIDIR = $(BINDIR)/ncbi else ifeq (--static,$(STATIC)) # in static builds, we are relative to binary path # because the configuration library will be part of tool NCBIDIR = $(BINDIR)/ncbi else # in dynamic builds, we are relative to library path # because the configuration library will live there NCBIDIR = $(LIBDIR)/ncbi endif endif # make reissue command MAKE_CMD = $(MAKE) BUILD=$(BUILD) COMP=$(COMP) TOP=$(TOP) \ SRCDIR=$(SRCDIR) OUTDIR=$(OUTDIR) -C $(OBJDIR) -f $(SRCDIR)/Makefile # directory and link creation SUBDIRS = bin ilib lib mod wmod OUTDIRS = schema # clean rules stdclean: @ rm -rf $(OBJDIR) @ rm -f $(addsuffix .vers.h,$(ALL_TOOLS) $(ALL_LIBS)) \ $(addsuffix .*,$(addprefix $(ILIBDIR)/,$(ALL_LIBS))) \ $(addsuffix .*,$(addprefix $(LIBDIR)/,$(ALL_LIBS))) \ $(addsuffix .*,$(addprefix $(MODDIR)/,$(ALL_LIBS))) \ $(addsuffix .*,$(addprefix $(WMODDIR)/,$(ALL_LIBS))) \ $(addsuffix *,$(addprefix $(BINDIR)/,$(ALL_TOOLS) $(ALL_LIBS))) # removing symbolic links that point to specific builds removelinks: @ test ! -h $(OUTDIR)/schema && rm -rf $(OUTDIR)/schema || true @ rm -f $(addprefix $(OUTDIR)/,$(addsuffix $(BITS),$(SUBDIRS))) @ rm -f $(addprefix $(OUTDIR)/,$(OUTDIRS)) # create all required output directories makedirs: @ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(NCBIDIR) ifeq (win,$(OS)) # Windows doesn't really support symbolic links # we may add them back in when our toolkit is able to create them rebuild-dirlinks: makedirs @ true else LNDIRS = $(addprefix ln_,$(SUBDIRS)) $(LNDIRS): @ ln -s $(TARGDIR)/$(subst ln_,,$@) $(OUTDIR)/$(subst ln_,,$@)$(BITS) rebuild-dirlinks: removelinks makedirs $(LNDIRS) @ ln -s $(TOP)/interfaces $(OUTDIR)/schema endif .PHONY: stdclean removelinks makedirs rebuild-dirlinks # configuration targets out: echo $(OUTDIR) > $(TOP)/build/OUTDIR.$(OS) @ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks CC: @ echo cc > $(TOP)/build/COMP.$(OS) @ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks GCC: @ echo gcc > $(TOP)/build/COMP.$(OS) @ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks ICC: @ echo icc > $(TOP)/build/COMP.$(OS) @ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks VC++: @ echo vc++ > $(TOP)/build/COMP.$(OS) @ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks debug: @ echo dbg > $(TOP)/build/BUILD.$(OS) @ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks profile: @ echo prof > $(TOP)/build/BUILD.$(OS) @ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks release: @ echo rel > $(TOP)/build/BUILD.$(OS) @ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks scm: @ echo scm > $(TOP)/build/BUILD.$(OS) @ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks pubtools: @ echo pub > $(TOP)/build/BUILD.$(OS) @ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks bindir: @ echo "$(BINDIR)" purify: @ echo pur > $(TOP)/build/BUILD.$(OS) @ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks purecov: @ echo pcov > $(TOP)/build/BUILD.$(OS) @ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks .PHONY: out CC GCC ICC debug profile release scm purify purecov # includes based upon build ITF = $(TOP)/interfaces OSINC = $(TOP)/interfaces/os CCINC = $(TOP)/interfaces/cc XTINC = $(TOP)/interfaces/ext # OS specific source and include dirs SRCDIRS_OS = $(SRCDIR)/$(OS) INCDIRS_OS = $(OSINC)/$(OS) # most OS' have a parent type ifdef OS_DAD SRCDIRS_OS += $(SRCDIR)/$(OS_DAD) INCDIRS_OS += $(OSINC)/$(OS_DAD) # some OS' have a grandparent ifdef OS_GDAD SRCDIRS_OS += $(SRCDIR)/$(OS_GDAD) INCDIRS_OS += $(OSINC)/$(OS_GDAD) endif endif # compiler specific includes INCDIRS_COMP = \ $(CCINC)/$(COMP)/$(ARCH) \ $(CCINC)/$(COMP) # some compilers have a parent type ifdef COMP_DAD INCDIRS_COMP += \ $(CCINC)/$(COMP_DAD)/$(ARCH) \ $(CCINC)/$(COMP_DAD) endif VPATH = \ $(SRCDIR)/$(COMP)/$(ARCH) \ $(SRCDIR)/$(COMP) \ $(SRCDIRS_OS) \ $(SRCDIR) INCDIRS = \ $(addprefix -I,$(SRCDIRS_OS)) \ $(addprefix -I,$(SRCDIR) $(ITF)) \ $(addprefix -I,$(INCDIRS_COMP)) \ $(addprefix -I,$(INCDIRS_OS) $(XTINC)) # defines that describe os & architecture DLLX ?= $(SHLX) ARCHDEFS = -D_ARCH_BITS=$(BITS) -DLIBPREFIX=$(LPFX) -DSHLIBEXT=$(DLLX) # default tool parameters CFLAGS = $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(LINKAGE) $(DEFINES) $(ARCHDEFS) $(INCDIRS) CPFLAGS = $(DEBUG) $(DBG) $(CARCH) $(PROF) $(LINKAGE) $(DEFINES) $(ARCHDEFS) $(INCDIRS) LDFLAGS = $(DBG) $(PROF) sra_sdk-2.1.7/build/Makefile.linux0000664001221300116200000000426511477026530016546 0ustar rodarmertrace# =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # default compiler ifeq (,$(COMP)) COMP = gcc endif # handle attempts to set cross-compilation architecture # note that if your installation is set up for cross compilation, # you can try to enable it on your own. ifeq (i386,$(ARCH)) i386: @ true x86_64: @ echo "Linux builds do not support cross-compilation to this architecture" endif ifeq (x86_64,$(ARCH)) i386: @ echo "Linux builds do not support cross-compilation to this architecture" x86_64: @ true endif .PHONY: i386 x86_64 # library prefix LPFX = lib # file extensions OBJX = o LOBX = pic.o LIBX = a SHLX = so # compilation defines DEFINES := -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 # linux is a Unix variant OS_DAD = unix # support for libxml ## TBD - move to libs/kxml, but this will break static builds... ifdef NCBI ifeq (dbg,$(BUILD)) LIBXML_LPATH = $(NCBI)/libxml/DebugMT/lib else LIBXML_LPATH = $(NCBI)/libxml/lib endif DFLT_LIBXML_INCLUDES = $(NCBI)/libxml/include/libxml2 endif sra_sdk-2.1.7/build/BUILD.linux0000644001221300116200000000000411625267705015657 0ustar rodarmertracepub sra_sdk-2.1.7/build/Makefile.rules0000644001221300116200000000642711476752037016550 0ustar rodarmertrace# =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== ## build rules # executable image %.$(OBJX): %.c $(CC) -o $@ $(OPT) $< %.$(OBJX): %.cpp $(CP) -o $@ $(OPT) $< %.$(OBJX): %.cxx $(CP) -o $@ $(OPT) $< # non-optimized executable image %.nopt.$(OBJX): %.c $(CC) -o $@ $(NOPT) $< %.nopt.$(OBJX): %.cpp $(CP) -o $@ $(NOPT) $< %.nopt.$(OBJX): %.cxx $(CP) -o $@ $(NOPT) $< # relocatable image %.$(LOBX): %.c $(CC) -o $@ -fPIC $(OPT) -D_LIBRARY $< %.$(LOBX): %.cpp $(CP) -o $@ -fPIC $(OPT) -D_LIBRARY $< %.$(LOBX): %.cxx $(CP) -o $@ -fPIC $(OPT) -D_LIBRARY $< # non-optimized relocatable image %.nopt.$(LOBX): %.c $(CC) -o $@ -fPIC $(NOPT) -D_LIBRARY $< %.nopt.$(LOBX): %.cpp $(CP) -o $@ -fPIC $(NOPT) -D_LIBRARY $< %.nopt.$(LOBX): %.cxx $(CP) -o $@ -fPIC $(NOPT) -D_LIBRARY $< # non-optimized relocatable image with persisted image byte swapping %.swap.nopt.$(LOBX): %.c $(CC) -o $@ -fPIC -DSWAP_PERSISTED $(NOPT) -D_LIBRARY $< %.swap.nopt.$(LOBX): %.cpp $(CP) -o $@ -fPIC -DSWAP_PERSISTED $(NOPT) -D_LIBRARY $< %.swap.nopt.$(LOBX): %.cxx $(CP) -o $@ -fPIC -DSWAP_PERSISTED $(NOPT) -D_LIBRARY $< # assembly %.$(OBJX) %.$(LOBX): %.s $(CC) -o $@ $< # assembly language output %.s: %.c $(CC) -S -o $@ $(OPT) $< %.s: %.cpp $(CP) -S -o $@ $(OPT) $< %.s: %.cxx $(CP) -S -o $@ $(OPT) $< %.nopt.s: %.c $(CC) -S -o $@ $(NOPT) $< %.nopt.s: %.cpp $(CP) -S -o $@ $(NOPT) $< %.nopt.s: %.cxx $(CP) -S -o $@ $(NOPT) $< %.pic.s: %.c $(CC) -S -o $@ -fPIC $(OPT) $< %.pic.s: %.cpp $(CP) -S -o $@ -fPIC $(OPT) $< %.pic.s: %.cxx $(CP) -S -o $@ -fPIC $(OPT) $< %.nopt.pic.s: %.c $(CC) -S -o $@ -fPIC $(NOPT) $< %.nopt.pic.s: %.cpp $(CP) -S -o $@ -fPIC $(NOPT) $< %.nopt.pic.s: %.cxx $(CP) -S -o $@ -fPIC $(NOPT) $< ###################################################################### ## TBD: *.vers.h will no longer be generated or used for executables # # instead, we will update the linker to produce a *.vers.o # # with a stub for KAppVersion to return a constant # ###################################################################### # version include generation %.vers.h: %.vers $(TOP)/build/make-vers-inc.sh $^ > $@ sra_sdk-2.1.7/build/Makefile.win0000644001221300116200000000335511625747372016212 0ustar rodarmertrace# =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # default compiler ifeq (,$(COMP)) COMP = vc++ endif # handle attempts to set cross-compilation architecture ifeq (i386,$(ARCH)) i386: @ true x86_64: @ echo "Windows builds do not support cross-compilation to this architecture" endif ifeq (x86_64,$(ARCH)) i386: @ echo "Windows builds do not support cross-compilation to this architecture" x86_64: @ true endif .PHONY: i386 x86_64 # library prefix LPFX = lib # file extensions OBJX = obj LOBX = pic.obj LIBX = a SHLX = lib DLLX = dll # compilation defines DEFINES := -DWINDOWS sra_sdk-2.1.7/build/abspath.sh0000755001221300116200000000242011506455277015725 0ustar rodarmertrace#!/bin/sh # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== if cd "$1" then pwd else echo "`pwd`/$1" fi sra_sdk-2.1.7/build/ld.linux.cmn.sh0000755001221300116200000000576611625212547016625 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # script name SELF_NAME="$(basename $0)" # parameters LD="$1" ARCH="$2" BUILD="$3" shift 3 SRCDIR="$1" BINDIR="$2" OUTDIR="$3" TARG="$4" NAME="$5" DBGAP="$6" shift 6 VERS="$1" VERSFILE="$2" DEPFILE="$3" shift 3 MODE="$1" SCMFLAGS="$2" LDFLAGS="$3" shift 3 LDIRS="$1" XDIRS="$2" shift 2 OBJS="$1" LIBS="$2" # decode MODE STATIC=$(expr $MODE % 2) MODE=$(expr $MODE / 2) DYLD=$(expr $MODE % 2) MODE=$(expr $MODE / 2) KPROC=$(expr $MODE % 2) THREADS=$(expr $MODE / 2) # decode SCMFLAGS CHECKSUM=$(expr $SCMFLAGS % 2) STATICSYSLIBS=$(expr $SCMFLAGS / 2) # return parameter for find-lib LIBPATH='' # initial command state CMD='' LD_STATIC_STATE=0 LD_ALL_STATE=0 # for breaking out version set-vers () { MAJ=$1 MIN=$2 REL=$3 } # for locating libraries find-lib () { _lib="lib$1" _dirs="$2" LIBPATH='' while [ "$_dirs" != "" ] do _dir="${_dirs%%:*}" if [ "$_dir" != "" ] then if [ -e "$_dir/$_lib" ] then while [ -L "$_dir/$_lib" ] do _lib=$(readlink -n "$_dir/$_lib") done LIBPATH="$_dir/$_lib" break; fi fi _dirs="${_dirs#$_dir}" _dirs="${_dirs#:}" done } # setting state load-static () { if [ $LD_STATIC_STATE -eq 0 ] then CMD="$CMD $LD_STATIC" LD_STATIC_STATE=1 fi } load-dynamic () { if [ $LD_STATIC_STATE -eq 1 ] then CMD="$CMD $LD_DYNAMIC" LD_STATIC_STATE=0 fi } load-all-symbols () { if [ $LD_ALL_STATE -eq 0 ] then CMD="$CMD $LD_ALL_SYMBOLS" LD_ALL_STATE=1 fi } load-ref-symbols () { if [ $LD_ALL_STATE -eq 1 ] then CMD="$CMD $LD_REF_SYMBOLS" LD_ALL_STATE=0 fi } sra_sdk-2.1.7/build/ld.linux.dlib.sh0000755001221300116200000001622011625212547016745 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # =========================================================================== # input library types, and their handling # # normal linkage # -l : find shared or static # -s : require static # -d : require shared # # static linkage # -l : require static # -s : require static # -d : ignore # =========================================================================== # script name SELF_NAME="$(basename $0)" BUILD_DIR="$(dirname $0)" # parameters and common functions source "${0%dlib.sh}cmn.sh" # discover tool chain case "$LD" in g*) source "${0%dlib.sh}gcc.sh" ;; i*) source "${0%dlib.sh}icc.sh" ;; *) echo "$SELF_NAME: unrecognized ld tool - '$LD'" exit 5 esac # DLIB_CMD was started in tool-specific source CMD="$DLIB_CMD $LDFLAGS" # tack on object files CMD="$CMD $OBJS" # list of static libraries used to create dynamic lib SLIBS='' # initial dependency upon Makefile and vers file DEPS="$SRCDIR/Makefile $VERSFILE" if [ "$LIBS" != "" ] then # tack on paths DIRS="$LDIRS:$XDIRS" while [ "$DIRS" != "" ] do DIR="${DIRS%%:*}" [ "$DIR" != "" ] && CMD="$CMD -L$DIR" DIRS="${DIRS#$DIR}" DIRS="${DIRS#:}" done # tack on libraries, finding as we go for LIB in $LIBS do # strip off switch LIBNAME="${LIB#-[lsd]}" # look at linkage case "$LIB" in -ldl|-ddl) # always load libdl as shared library load-ref-symbols load-dynamic CMD="$CMD -ldl" ;; -l*) # normal or dynamic linkage FOUND=0 if [ $STATIC -eq 0 ] then find-lib $LIBNAME.so $LDIRS if [ "$LIBPATH" != "" ] then # found it FOUND=1 # load normally load-ref-symbols load-dynamic CMD="$CMD -l$LIBNAME" fi fi # try static only if [ $FOUND -eq 0 ] then find-lib $LIBNAME.a $LDIRS if [ "$LIBPATH" != "" ] then # found it FOUND=1 # add it to dependencies DEPS="$DEPS $LIBPATH" SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a" # load static load-static load-all-symbols CMD="$CMD -l$LIBNAME" fi fi # not found within our directories if [ $FOUND -eq 0 ] then if [ $STATICSYSLIBS -eq 1 ] then case "$LIBNAME" in z|bz2) # set load to static load-static load-all-symbols ;; *) # set load to dynamic load-ref-symbols load-dynamic ;; esac else # set load to normal load-ref-symbols load-dynamic fi CMD="$CMD -l$LIBNAME" fi ;; -s*) # force static load FOUND=0 find-lib $LIBNAME.a $LDIRS if [ "$LIBPATH" != "" ] then # found it FOUND=1 # add it to dependencies DEPS="$DEPS $LIBPATH" SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a" # load static load-static load-all-symbols CMD="$CMD -l$LIBNAME" fi # not found within our directories if [ $FOUND -eq 0 ] then if [ $STATIC -eq 1 ] || [ $STATICSYSLIBS -eq 1 ] then # set load to static load-static load-all-symbols else case "$LIBNAME" in z|bz2) # set load to dynamic load-ref-symbols load-dynamic ;; *) # set load to static load-static load-all-symbols ;; esac fi CMD="$CMD -l$LIBNAME" fi ;; -d*) # only dynamic linkage FOUND=0 if [ $STATIC -eq 0 ] then find-lib $LIBNAME.so $LDIRS if [ "$LIBPATH" != "" ] then # found it FOUND=1 # load normally load-ref-symbols load-dynamic CMD="$CMD -l$LIBNAME" fi fi # not found within our directories if [ $FOUND -eq 0 ] then # set load to normal load-ref-symbols load-dynamic CMD="$CMD -l$LIBNAME" fi ;; esac done fi # put state back to normal load-ref-symbols load-dynamic # add in pthreads if [ $THREADS -ne 0 ] then CMD="$CMD -lpthread" fi # produce shared library echo "$CMD" $CMD || exit $? # produce dependencies if [ "$DEPFILE" != "" ] then echo "$TARG: $DEPS" > "$DEPFILE" fi if [ $CHECKSUM -eq 1 ] then SCM_DIR="${BUILD_DIR%/*}/scm" LOGFILE="$SCM_DIR/scm.log" MSG=">>>>> scm: calling the collect script from ld.linux.dlib.sh <<<<<<" #echo "$MSG" echo "$MSG" >> $LOGFILE "$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5" fisra_sdk-2.1.7/build/increment-release.sh0000755001221300116200000000275711506455277017722 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # capture input VERSION=$1 # split the version into separate integers SPLIT_VERS="$(echo $VERSION | tr '.' ' ')" inc-version () { local MAJ=$1 local MIN=$2 local REL=$(expr $3 + 1) echo "$MAJ.$MIN.$REL" } # rewrite the version inc-version $SPLIT_VERS sra_sdk-2.1.7/build/ld.linux.gcc.sh0000755001221300116200000000343111506455277016576 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # define linker params LD_EXPORT_GLOBAL="-Wl,--export-dynamic" LD_MULTIPLE_DEFS="-Wl,-zmuldefs" LD_STATIC="-Wl,-Bstatic" LD_DYNAMIC="-Wl,-Bdynamic" LD_ALL_SYMBOLS="-Wl,-whole-archive" LD_REF_SYMBOLS="-Wl,-no-whole-archive" # build command DLIB_CMD="$LD -shared" EXE_CMD="$LD" # versioned output if [ "$VERS" = "" ] then DLIB_CMD="$DLIB_CMD -o $TARG" EXE_CMD="$EXE_CMD -o $TARG" else set-vers $(echo $VERS | tr '.' ' ') DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ" EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS" fi sra_sdk-2.1.7/build/ld.linux.icc.sh0000755001221300116200000000342111506455277016577 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # define linker params LD_EXPORT_GLOBAL="-Wa,--export-dynamic" LD_MULTIPLE_DEFS="-Wa,-zmuldefs" LD_STATIC="-Bstatic" LD_DYNAMIC="-Bdynamic" LD_ALL_SYMBOLS="-Wa,-whole-archive" LD_REF_SYMBOLS="-Wa,-no-whole-archive" # build command DLIB_CMD="$LD -shared" EXE_CMD="$LD" # versioned output if [ "$VERS" = "" ] then DLIB_CMD="$DLIB_CMD -o $TARG" EXE_CMD="$EXE_CMD -o $TARG" else set-vers $(echo $VERS | tr '.' ' ') DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ" EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS" fi sra_sdk-2.1.7/build/ld.mac.gcc.sh0000755001221300116200000000374211576721671016205 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # define linker params LD_EXPORT_GLOBAL="-Wl,-all_load" LD_MULTIPLE_DEFS="" LD_STATIC="" LD_DYNAMIC="" LD_ALL_SYMBOLS="" LD_REF_SYMBOLS="" # the Mac is set up for cross-compilation LD="$LD -Wl,-arch,$ARCH" # build command DLIB_CMD="$LD -dynamiclib" EXE_CMD="$LD" # Mach install-name sans extension INSTNAME="@executable_path/../lib/$NAME$DBGAP" # versioned output if [ "$VERS" = "" ] then DLIB_CMD="$DLIB_CMD -o $TARG -install_name $INSTNAME.dylib" EXE_CMD="$EXE_CMD -o $TARG" else set-vers $(echo $VERS | tr '.' ' ') DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.$VERS.dylib -install_name $INSTNAME.$VERS.dylib -compatibility_version $MAJ -current_version $VERS -flat_namespace -undefined suppress" EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS" fi sra_sdk-2.1.7/build/make-vers-inc.sh0000755001221300116200000000317411506455277016753 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # capture input if [ $# -eq 1 ] then VERSION=$1 DEFINE=$(basename $VERSION) DEFINE=$(echo $DEFINE | tr '[a-z].-' '[A-Z]__') elif [ $# -ne 2 ] then echo "#error in makefile" exit 1 else DEFINE=$1 VERSION=$2 fi # split the version into separate integers SPLIT_VERS="$(cat $VERSION | tr '.' ' ')" # issue a single line define echo "#define $DEFINE $(printf 0x%02X%02X%04X $SPLIT_VERS)" sra_sdk-2.1.7/build/STATIC0000664001221300116200000000000011543170350014633 0ustar rodarmertracesra_sdk-2.1.7/build/cc.sh0000755001221300116200000000570011550612416014661 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # prepare script name SELF_NAME="$(basename $0)" SCRIPT_BASE="${0%.sh}" # os OS="$1" shift # binary compiler CC="$1" shift # configuration unset TARG unset ARGS CHECKSUM=0 OBJX=o while [ $# -ne 0 ] do case "$1" in --cflags) ARGS="$ARGS $2" shift ;; --checksum) CHECKSUM=1 ;; --objx) OBJX="$2" shift ;; -o*) ARGS="$ARGS $1" ARG="${1#-o}" if [ "$ARG" = "" ] then ARGS="$ARGS $2" ARG="$2" shift fi TARG="$ARG" ;; *) ARGS="$ARGS $1" ;; esac shift done # *** START SCM-code *************************************** if [ $CHECKSUM -eq 1 ] then if [ "$TARG" = "" ] then echo "$SELF_NAME: no target specified" exit 5 fi if [ "$TARG" = "${TARG%.$OBJX}" ] then echo "$SELF_NAME: malformed target" exit 6 fi TARG="${TARG%.$OBJX}" fi # *** END SCM-code *************************************** CMD="$CC $ARGS" echo "$CMD" $CMD || exit $? # *** START SCM-code *************************************** if [ $CHECKSUM -eq 1 ] && [ "$OS" = "linux" ] then CMD="strip $TARG.$OBJX -o $TARG.stripped.$OBJX" echo "$CMD" if $CMD then MD5RES=`md5sum -b $TARG.stripped.$OBJX` STATUS=$? rm -f "$TARG.stripped.$OBJX" || true if [ $STATUS -eq 0 ] then MD5VALUE=${MD5RES:0:32} echo "$TARG.$OBJX=$MD5VALUE" > "$TARG.$OBJX.md5" else exit $STATUS fi else STATUS=$? rm "$TARG.$OBJX" exit $STATUS fi fi # *** END SCM-code *************************************** sra_sdk-2.1.7/build/BUILD.mac0000644001221300116200000000000411625267705015260 0ustar rodarmertracepub sra_sdk-2.1.7/build/Makefile.vc++0000644001221300116200000000503611630010446016126 0ustar rodarmertrace# =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # compilers CC = @ $(TOP)/build/win-cc.sh win "cl /c -D_WIN32_WINNT=0x0502" \ $(CHECKSUM) --objx $(OBJX) $(CFLAGS) -MD CP = @ $(TOP)/build/win-cc.sh win "cl /c" \ $(CHECKSUM) --objx $(OBJX) $(CPFLAGS) -MD # C preprocessor PP = gcc -E $(CFLAGS) # linkers LD = @ $(TOP)/build/ld.sh win $(ARCH) link \ --build $(BUILD) $(LDFLAGS) $(STATIC) $(CHECKSUM) \ --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) LP = @ $(TOP)/build/ld.sh win $(ARCH) link \ --build $(BUILD) $(LDFLAGS) $(STATIC) $(CHECKSUM) \ --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) # tool options CDECL = -Gd STDCALL = -Gz CALLCONV = $(STDCALL) STRING_POOLING = -GF OPT := $(STRING_POOLING) $(CALLCONV) -nologo NOPT := -Od $(OPT) ifeq (64,$(BITS)) CARCH = #-m64 else CARCH = #-m32 WARN := #-Wall endif ifeq (prof, $(BUILD)) # PROF := -pg endif ifeq (dbg, $(BUILD)) DBG = -Od OPT += -Zi $(WARN) NOPT += -Zi $(WARN) else # -Ox caused us failures noticed in libs/vdb/cast.c # OPT += -Ox -w # /Ox == /Ob2gity g is deprecated so removed # Removing either the 2 or the t makes it seem to work # But there is a warning about not knowing what /Ob is # if the 2 is removed. But not if the 2 is there. # Woo hoo Microsoft... OPT += -Ob2iy -w endif sra_sdk-2.1.7/build/Makefile.shell0000664001221300116200000000505611550613203016504 0ustar rodarmertrace# =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # determine OS UNAME = $(shell uname -s) ifeq (Darwin, $(UNAME)) OS = mac endif ifeq (Linux, $(UNAME)) OS = linux endif ifeq (SunOS, $(UNAME)) OS = sun endif ifeq (xCYGWIN, $(findstring xCYGWIN,x$(UNAME))) OS = win endif ifeq (xMINGW, $(findstring xMINGW,x$(UNAME))) OS = win endif # OS flavor is normally OS OSFLAV = $(OS) # determine ARCH ifeq (mac,$(OS)) ARCH = $(shell $(TOP)/build/mac.arch.sh) else MARCH = $(shell uname -m) ifeq (i386, $(MARCH)) ARCH = i386 endif ifeq (i486, $(MARCH)) ARCH = i386 endif ifeq (i586, $(MARCH)) ARCH = i386 endif ifeq (i686, $(MARCH)) ARCH = i386 endif ifeq (x86_64, $(MARCH)) ARCH = x86_64 endif ifeq (sun4u,$(MARCH)) ARCH = sparc32 endif endif # determine BITS ifeq (x86_64, $(ARCH)) BITS = 64 else BITS = 32 endif # first pass through defines SRCDIR ifndef SRCDIR # set SRCDIR from MODULE ifdef MODULE SRCDIR=$(TOP)/$(MODULE) else SRCDIR=$(TOP) endif # set OUTDIR ifndef OUTDIR OUTDIR = $(shell test -f $(TOP)/build/OUTDIR.$(OS) && cat $(TOP)/build/OUTDIR.$(OS) || echo $(TOP)) ifeq (,$(OUTDIR)) OUTDIR = $(TOP) endif ifeq (.,$(OUTDIR)) OUTDIR = $(TOP) endif endif # set COMP and BUILD COMP = $(shell test -f $(TOP)/build/COMP.$(OS) && cat $(TOP)/build/COMP.$(OS) || echo gcc) BUILD = $(shell test -f $(TOP)/build/BUILD.$(OS) && cat $(TOP)/build/BUILD.$(OS) || echo dbg) endif sra_sdk-2.1.7/build/COMP.linux0000644001221300116200000000000411542740620015544 0ustar rodarmertracegcc sra_sdk-2.1.7/build/Makefile.gcc0000644001221300116200000000442611577656545016160 0ustar rodarmertrace# =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # compilers CC = @ $(TOP)/build/cc.sh $(OS) 'gcc -c' \ $(CHECKSUM) --objx $(OBJX) --cflags "$(CFLAGS)" -MD CP = @ $(TOP)/build/cc.sh $(OS) 'g++ -c' \ $(CHECKSUM) --objx $(OBJX) --cflags "$(CPFLAGS)" -MD # C preprocessor PP = gcc -E $(CFLAGS) # linkers LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \ --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \ --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) # tool options WARN = -Wall # -Wconversion ifeq (64,$(BITS)) CARCH = -m64 else CARCH = -m32 endif ifeq (prof, $(BUILD)) PROF = -pg endif ifeq (dbg, $(BUILD)) DBG = -g OPT = $(WARN) NOPT = $(WARN) PED = -std=c99 -ansi -pedantic else ifeq (x86_64, $(ARCH)) OPT = -O3 -fno-strict-aliasing else OPT = -O3 -fno-strict-aliasing endif endif sra_sdk-2.1.7/build/Makefile.icc0000644001221300116200000000450211556621613016136 0ustar rodarmertrace# =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # compilers CC = @ $(TOP)/build/cc.sh $(OS) 'icc -c' \ $(CHECKSUM) --objx $(OBJX) --cflags "$(CFLAGS)" -MD CP = @ $(TOP)/build/cc.sh $(OS) 'icpc -c' \ $(CHECKSUM) --objx $(OBJX) --cflags "$(CPFLAGS)" -MD # C preprocessor PP = icc -E $(CFLAGS) # linkers LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) icc \ --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) icpc \ --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) # tool options WARN = -Wall ifeq (64,$(BITS)) CARCH = -m64 else CARCH = -m32 endif ifeq (prof, $(BUILD)) PROF := -p endif ifeq (dbg, $(BUILD)) DBG = -g OPT = $(WARN) NOPT = $(WARN) else ifeq (x86_64, $(ARCH)) OPT := -O3 -unroll -xW else OPT := -O3 -unroll -xW endif endif ifeq (prof, $(BUILD)) OPT += -vec_report5 endif # ICC is designed to be a GCC substitute COMP_DAD = gcc sra_sdk-2.1.7/build/ld.linux.exe.sh0000775001221300116200000001707411625212547016626 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # =========================================================================== # input library types, and their handling # # normal linkage # -l : find shared or static # -s : require static # -d : ignore - will be dynamically loaded # # static linkage # -l : require static # -s : require static # -d : require static # =========================================================================== # script name SELF_NAME="$(basename $0)" BUILD_DIR="$(dirname $0)" # parameters and common functions source "${0%exe.sh}cmn.sh" # discover tool chain case "$LD" in g*) source "${0%exe.sh}gcc.sh" ;; i*) source "${0%exe.sh}icc.sh" ;; *) echo "$SELF_NAME: unrecognized ld tool - '$LD'" exit 5 esac # EXE_CMD was started in tool-specific source CMD="$EXE_CMD $LDFLAGS" # if building a static executable against dynamic libraries # the main application will substitute for name lookup if [ $STATIC -eq 1 ] && [ $DYLD -eq 1 ] then CMD="$CMD $LD_EXPORT_GLOBAL $LD_MULTIPLE_DEFS" fi # tack on object files CMD="$CMD $OBJS" # list of static libraries used to create executable SLIBS='' # initial dependency upon Makefile and vers file DEPS="$SRCDIR/Makefile $VERSFILE" if [ "$LIBS" != "" ] then # tack on paths DIRS="$LDIRS:$XDIRS" while [ "$DIRS" != "" ] do DIR="${DIRS%%:*}" [ "$DIR" != "" ] && CMD="$CMD -L$DIR" DIRS="${DIRS#$DIR}" DIRS="${DIRS#:}" done # tack on libraries, finding as we go for LIB in $LIBS do # strip off switch LIBNAME="${LIB#-[lsd]}" # look at linkage case "$LIB" in -ldl|-ddl) # always load libdl as shared library load-ref-symbols load-dynamic CMD="$CMD -ldl" ;; -l*) # normal or dynamic linkage FOUND=0 if [ $STATIC -eq 0 ] then find-lib $LIBNAME.so $LDIRS if [ "$LIBPATH" != "" ] then # found it FOUND=1 # load dynamic load-dynamic CMD="$CMD -l$LIBNAME" fi fi # try static only if [ $FOUND -eq 0 ] then find-lib $LIBNAME.a $LDIRS if [ "$LIBPATH" != "" ] then # found it FOUND=1 # add it to dependencies DEPS="$DEPS $LIBPATH" SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a" # load static load-static [ $STATIC -eq 1 ] && load-all-symbols CMD="$CMD -l$LIBNAME" fi fi # not found within our directories if [ $FOUND -eq 0 ] then # do not need to load all symbols for external libs [ $STATIC -eq 1 ] && load-ref-symbols if [ $STATICSYSLIBS -eq 1 ] then case "$LIBNAME" in z|bz2) # set load to static load-static ;; *) # set load to dynamic load-dynamic ;; esac else # set load to normal load-dynamic fi CMD="$CMD -l$LIBNAME" fi ;; -s*) # force static load FOUND=0 find-lib $LIBNAME.a $LDIRS if [ "$LIBPATH" != "" ] then # found it FOUND=1 # add it to dependencies DEPS="$DEPS $LIBPATH" SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a" # load static load-static [ $STATIC -eq 1 ] && load-all-symbols CMD="$CMD -l$LIBNAME" fi # not found within our directories if [ $FOUND -eq 0 ] then # do not need to load all symbols for external libs [ $STATIC -eq 1 ] && load-ref-symbols if [ $STATIC -eq 1 ] || [ $STATICSYSLIBS -eq 1 ] then # set load to static load-static else # special case for libs we have in "ext" # that are sometimes requested as static case "$LIBNAME" in z|bz2) # set load to dynamic load-dynamic ;; *) load-static ;; esac fi CMD="$CMD -l$LIBNAME" fi ;; -d*) FOUND=0 if [ $STATIC -eq 1 ] then find-lib $LIBNAME.a $LDIRS if [ "$LIBPATH" != "" ] then # found it FOUND=1 # add it to dependencies DEPS="$DEPS $LIBPATH" SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a" # load static load-static load-all-symbols CMD="$CMD -l$LIBNAME" fi # not found within our directories if [ $FOUND -eq 0 ] then load-static load-all-symbols CMD="$CMD -l$LIBNAME" fi fi ;; esac done fi # return to normal load-ref-symbols load-dynamic # add in pthreads if [ $THREADS -ne 0 ] then CMD="$CMD -lpthread" fi # produce shared library echo $CMD $CMD || exit $? # produce dependencies if [ "$DEPFILE" != "" ] then echo "$TARG: $DEPS" > "$DEPFILE" fi if [ $CHECKSUM -eq 1 ] then SCM_DIR="${BUILD_DIR%/*}/scm" LOGFILE="$SCM_DIR/scm.log" MSG=">>>>> scm: calling the collect script from ld.linux.exe.sh <<<<<<" #echo "$MSG" echo "$MSG" >> $LOGFILE "$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5" fi sra_sdk-2.1.7/build/ld.linux.ln.sh0000755001221300116200000000437511506455277016463 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # script name SELF_NAME="$(basename $0)" # parameters TYPE="$1" OUTDIR="$2" TARG="$3" NAME="$4" DBGAP="$5" EXT="$6" VERS="$7" # find target TARG=$(basename "$TARG") # put extension back onto name NAME="$NAME$DBGAP" [ "$EXT" != "" ] && NAME="$NAME.$EXT" # break out version set-vers () { MAJ=$1 MIN=$2 REL=$3 } set-vers $(echo $VERS | tr '.' ' ') cd "$OUTDIR" || exit 5 # create link create-link () { rm -f "$2" local CMD="ln -s $1 $2" echo $CMD $CMD } # test for version in target name if [ "$TARG" != "$NAME.$MAJ.$MIN.$REL" ] then # for simple name, create 2 links if [ "$TARG" = "$NAME" ] then create-link "$NAME.$MAJ.$MIN.$REL" "$NAME.$MAJ" create-link "$NAME.$MAJ" "$NAME" # for name with major version in it elif [ "$TARG" = "$NAME.$MAJ" ] then create-link "$NAME.$MAJ.$MIN.$REL" "$NAME.$MAJ" # for name with major & minor version in it elif [ "$TARG" = "$NAME.$MAJ.$MIN" ] then create-link "$NAME.$MAJ.$MIN.$REL" "$NAME.$MAJ.$MIN" fi fi sra_sdk-2.1.7/build/ld.linux.slib.sh0000755001221300116200000000725511550612416016770 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # =========================================================================== # input library types, and their handling # # normal or static linkage # -l : require static # -s : require static # -d : ignore # =========================================================================== # script name SELF_NAME="$(basename $0)" BUILD_DIR="$(dirname $0)" # parameters and common functions source "${0%slib.sh}cmn.sh" # initialize command CMD="ar -rc" # function to convert an archive into individual object files convert-static () { # list members local path="$1" local mbrs="$(ar -t $path)" # unpack archive into temporary directory mkdir -p ld-tmp if ! cd ld-tmp then echo "$SELF_NAME: failed to cd to ld-tmp" exit 5 fi ar -x "$path" # rename and add to source files list local m= for m in $mbrs do mv $m $NAME-$m CMD="$CMD ld-tmp/$NAME-$m" done # return to prior location cd - > /dev/null } # versioned output if [ "$VERS" = "" ] then CMD="$CMD $TARG" else set-vers $(echo $VERS | tr '.' ' ') CMD="$CMD $OUTDIR/$NAME$DBGAP.a.$VERS" fi # tack on object files CMD="$CMD $OBJS" # list of static libraries used to create this lib SLIBS='' # initial dependency upon Makefile and vers file DEPS="$SRCDIR/Makefile $VERSFILE" if [ "$LIBS" != "" ] then # tack on libraries, finding as we go for LIB in $LIBS do # strip off switch LIBNAME="${LIB#-[lsd]}" # look at linkage case "$LIB" in -l*|-s*) # force static load LIBPATH="$(find-lib $LIBNAME.a $LDIRS)" if [ "$LIBPATH" != "" ] then # add it to dependencies DEPS="$DEPS $LIBPATH" SLIBS="$SLIBS $(dirname $LIBPATH)/lib$LIBNAME.a" # convert to individual object files convert-static "$LIBPATH" || exit $? fi ;; esac done fi # produce static library echo $CMD $CMD || exit $? # remove temporaries rm -rf ld-tmp # produce dependencies if [ "$DEPFILE" != "" ] && [ "$DEPS" != "" ] then echo "$TARG: $DEPS" > "$DEPFILE" fi if [ $CHECKSUM -eq 1 ] then SCM_DIR="${BUILD_DIR%/*}/scm" LOGFILE="$SCM_DIR/scm.log" MSG=">>>>> scm: calling the collect script from ld.linux.slib.sh <<<<<<" #echo "$MSG" echo "$MSG" >> $LOGFILE "$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5" fi sra_sdk-2.1.7/build/ld.mac.cmn.sh0000755001221300116200000000571711625212547016222 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # script name SELF_NAME="$(basename $0)" # parameters LD="$1" ARCH="$2" BUILD="$3" shift 3 SRCDIR="$1" BINDIR="$2" OUTDIR="$3" TARG="$4" NAME="$5" DBGAP="$6" shift 6 VERS="$1" VERSFILE="$2" DEPFILE="$3" shift 3 MODE="$1" CHECKSUM="$2" LDFLAGS="$3" shift 3 LDIRS="$1" XDIRS="$2" shift 2 OBJS="$1" LIBS="$2" # decode MODE STATIC=$(expr $MODE % 2) MODE=$(expr $MODE / 2) DYLD=$(expr $MODE % 2) MODE=$(expr $MODE / 2) KPROC=$(expr $MODE % 2) THREADS=$(expr $MODE / 2) # return parameter for find-lib LIBPATH='' # initial command state CMD='' LD_STATIC_STATE=0 LD_ALL_STATE=0 # for breaking out version set-vers () { MAJ=$1 MIN=$2 REL=$3 } # for locating libraries find-lib () { _lib="lib$1" _dirs="$2" LIBPATH='' while [ "$_dirs" != "" ] do _dir="${_dirs%%:*}" if [ "$_dir" != "" ] then if [ -e "$_dir/$_lib" ] then while [ -L "$_dir/$_lib" ] do _lib=$(readlink -n "$_dir/$_lib") done LIBPATH="$_dir/$_lib" break; fi fi _dirs="${_dirs#$_dir}" _dirs="${_dirs#:}" done } # setting state load-static () { if [ $LD_STATIC_STATE -eq 0 ] then CMD="$CMD $LD_STATIC" LD_STATIC_STATE=1 fi } load-dynamic () { if [ $LD_STATIC_STATE -eq 1 ] then CMD="$CMD $LD_DYNAMIC" LD_STATIC_STATE=0 fi } load-all-symbols () { if [ $LD_ALL_STATE -eq 0 ] then CMD="$CMD $LD_ALL_SYMBOLS" # the Mac linker doesn't support state LD_ALL_STATE=0 fi } load-ref-symbols () { if [ $LD_ALL_STATE -eq 1 ] then CMD="$CMD $LD_REF_SYMBOLS" LD_ALL_STATE=0 fi } sra_sdk-2.1.7/build/ld.mac.dlib.sh0000755001221300116200000001252411506455277016360 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # =========================================================================== # input library types, and their handling # # normal linkage # -l : find shared or static # -s : require static # -d : require shared # # static linkage # -l : require static # -s : require static # -d : ignore # =========================================================================== # script name SELF_NAME="$(basename $0)" # parameters and common functions source "${0%dlib.sh}cmn.sh" # discover tool chain case "$LD" in g*) source "${0%dlib.sh}gcc.sh" ;; i*) source "${0%dlib.sh}icc.sh" ;; *) echo "$SELF_NAME: unrecognized ld tool - '$LD'" exit 5 esac # DLIB_CMD was started in tool-specific source CMD="$DLIB_CMD $LDFLAGS" # tack on object files CMD="$CMD $OBJS" # initial dependency upon Makefile and vers file DEPS="$SRCDIR/Makefile $VERSFILE" if [ "$LIBS" != "" ] then # tack on paths DIRS="$LDIRS:$XDIRS" while [ "$DIRS" != "" ] do DIR="${DIRS%%:*}" [ "$DIR" != "" ] && CMD="$CMD -L$DIR" DIRS="${DIRS#$DIR}" DIRS="${DIRS#:}" done # tack on libraries, finding as we go for LIB in $LIBS do # strip off switch LIBNAME="${LIB#-[lsd]}" # look at linkage case "$LIB" in -l*) # normal or dynamic linkage FOUND=0 if [ $STATIC -eq 0 ] then find-lib $LIBNAME.so $LDIRS if [ "$LIBPATH" != "" ] then # found it FOUND=1 # load normally load-ref-symbols load-dynamic CMD="$CMD -l$LIBNAME" fi fi # try static only if [ $FOUND -eq 0 ] then find-lib $LIBNAME.a $LDIRS if [ "$LIBPATH" != "" ] then # found it FOUND=1 # add it to dependencies DEPS="$DEPS $LIBPATH" # load static load-static load-all-symbols CMD="$CMD -l$LIBNAME" fi fi # not found within our directories if [ $FOUND -eq 0 ] then # set load to normal load-ref-symbols load-dynamic CMD="$CMD -l$LIBNAME" fi ;; -s*) # force static load FOUND=0 find-lib $LIBNAME.a $LDIRS if [ "$LIBPATH" != "" ] then # found it FOUND=1 # add it to dependencies DEPS="$DEPS $LIBPATH" # load static load-static load-all-symbols CMD="$CMD -l$LIBNAME" fi # not found within our directories if [ $FOUND -eq 0 ] then # set load to static load-static load-all-symbols CMD="$CMD -l$LIBNAME" fi ;; -d*) # only dynamic linkage FOUND=0 if [ $STATIC -eq 0 ] then find-lib $LIBNAME.so $LDIRS if [ "$LIBPATH" != "" ] then # found it FOUND=1 # load normally load-ref-symbols load-dynamic CMD="$CMD -l$LIBNAME" fi fi # not found within our directories if [ $FOUND -eq 0 ] then # set load to normal load-ref-symbols load-dynamic CMD="$CMD -l$LIBNAME" fi ;; esac done fi # put state back to normal load-ref-symbols load-dynamic # produce shared library echo $CMD $CMD || exit $? # produce dependencies if [ "$DEPFILE" != "" ] then echo "$TARG: $DEPS" > "$DEPFILE" fi sra_sdk-2.1.7/build/ld.mac.exe.sh0000755001221300116200000001271311576721672016231 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # =========================================================================== # input library types, and their handling # # normal linkage # -l : find shared or static # -s : require static # -d : ignore - will be dynamically loaded # # static linkage # -l : require static # -s : require static # -d : require static # =========================================================================== # script name SELF_NAME="$(basename $0)" # parameters and common functions source "${0%exe.sh}cmn.sh" # discover tool chain case "$LD" in g*) source "${0%exe.sh}gcc.sh" ;; i*) source "${0%exe.sh}icc.sh" ;; *) echo "$SELF_NAME: unrecognized ld tool - '$LD'" exit 5 esac # EXE_CMD was started in tool-specific source CMD="$EXE_CMD $LDFLAGS" # if building a static executable against dynamic libraries # the main application will substitute for name lookup if [ $STATIC -eq 1 ] && [ $DYLD -eq 1 ] then CMD="$CMD $LD_EXPORT_GLOBAL $LD_MULTIPLE_DEFS" fi # tack on object files CMD="$CMD $OBJS" # initial dependency upon Makefile and vers file DEPS="$SRCDIR/Makefile $VERSFILE" if [ "$LIBS" != "" ] then # tack on paths DIRS="$LDIRS:$XDIRS" while [ "$DIRS" != "" ] do DIR="${DIRS%%:*}" [ "$DIR" != "" ] && CMD="$CMD -L$DIR" DIRS="${DIRS#$DIR}" DIRS="${DIRS#:}" done # tack on libraries, finding as we go for LIB in $LIBS do # strip off switch LIBNAME="${LIB#-[lsd]}" # look at linkage case "$LIB" in -l*) # normal or dynamic linkage FOUND=0 if [ $STATIC -eq 0 ] then find-lib $LIBNAME.dylib $LDIRS if [ "$LIBPATH" != "" ] then # found it FOUND=1 # load dynamic load-dynamic CMD="$CMD -l$LIBNAME" fi fi # try static only if [ $FOUND -eq 0 ] then find-lib $LIBNAME.a $LDIRS if [ "$LIBPATH" != "" ] then # found it FOUND=1 # add it to dependencies DEPS="$DEPS $LIBPATH" # load static CMD="$CMD $LIBPATH" fi fi # not found within our directories if [ $FOUND -eq 0 ] then [ $STATIC -eq 1 ] && load-ref-symbols load-dynamic CMD="$CMD -l$LIBNAME" fi ;; -s*) # force static load FOUND=0 find-lib $LIBNAME.a $LDIRS if [ "$LIBPATH" != "" ] then # found it FOUND=1 # add it to dependencies DEPS="$DEPS $LIBPATH" # load library directly CMD="$CMD $LIBPATH" fi # not found within our directories if [ $FOUND -eq 0 ] then # set load to static load-static [ $STATIC -eq 1 ] && load-all-symbols CMD="$CMD -l$LIBNAME" fi ;; -d*) FOUND=0 if [ $STATIC -eq 1 ] then find-lib $LIBNAME.a $LDIRS if [ "$LIBPATH" != "" ] then # found it FOUND=1 # add it to dependencies DEPS="$DEPS $LIBPATH" # load static load-static load-all-symbols CMD="$CMD $LIBPATH" fi # not found within our directories if [ $FOUND -eq 0 ] then load-static load-all-symbols CMD="$CMD -l$LIBNAME" fi fi ;; esac done fi # return to normal load-ref-symbols load-dynamic # produce shared library echo $CMD $CMD || exit $? # produce dependencies if [ "$DEPFILE" != "" ] then echo "$TARG: $DEPS" > "$DEPFILE" fi sra_sdk-2.1.7/build/ld.mac.ln.sh0000755001221300116200000000501211506455277016051 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # script name SELF_NAME="$(basename $0)" # parameters TYPE="$1" OUTDIR="$2" TARG="$3" NAME="$4" DBGAP="$5" EXT="$6" VERS="$7" # find target TARG=$(basename "$TARG") # put extension back onto name, unless it's "dylib" NAME="$NAME$DBGAP" [ "$EXT" != "" ] && [ "$EXT" != "dylib" ] && NAME="$NAME.$EXT" # break out version set-vers () { MAJ=$1 MIN=$2 REL=$3 } set-vers $(echo $VERS | tr '.' ' ') cd "$OUTDIR" || exit 5 # assemble versioned names NAME_MMR="$NAME.$MAJ.$MIN.$REL" NAME_MM="$NAME.$MAJ.$MIN" NAME_M="$NAME.$MAJ" # if extension was "dylib", NOW append to names if [ "$EXT" = "dylib" ] then NAME_MMR="$NAME_MMR.$EXT" NAME_MM="$NAME_MM.$EXT" NAME_M="$NAME_M.$EXT" NAME="$NAME.$EXT" fi # create link create-link () { rm -f "$2" local CMD="ln -s $1 $2" echo $CMD $CMD } # test for version in target name if [ "$TARG" != "$NAME_MMR" ] then # for simple name, create 2 links if [ "$TARG" = "$NAME" ] then create-link "$NAME_MMR" "$NAME_M" create-link "$NAME_M" "$NAME" # for name with major version in it elif [ "$TARG" = "$NAME_M" ] then create-link "$NAME_MMR" "$NAME_M" # for name with major & minor version in it elif [ "$TARG" = "$NAME_MM" ] then create-link "$NAME_MMR" "$NAME_MM" fi fi sra_sdk-2.1.7/build/ld.mac.slib.sh0000755001221300116200000000636011506455277016400 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # =========================================================================== # input library types, and their handling # # normal or static linkage # -l : require static # -s : require static # -d : ignore # =========================================================================== # script name SELF_NAME="$(basename $0)" # parameters and common functions source "${0%slib.sh}cmn.sh" # initialize command CMD="ar -rc" # function to convert an archive into individual object files convert-static () { # list members local path="$1" local mbrs="$(ar -t $path)" # unpack archive into temporary directory mkdir -p ld-tmp if ! cd ld-tmp then echo "$SELF_NAME: failed to cd to ld-tmp" exit 5 fi ar -x "$path" # rename and add to source files list local m= for m in $mbrs do mv $m $NAME-$m CMD="$CMD ld-tmp/$NAME-$m" done # return to prior location cd - > /dev/null } # versioned output if [ "$VERS" = "" ] then CMD="$CMD $TARG" else set-vers $(echo $VERS | tr '.' ' ') CMD="$CMD $OUTDIR/$NAME$DBGAP.a.$VERS" fi # tack on object files CMD="$CMD $OBJS" # initial dependency upon Makefile and vers file DEPS="$SRCDIR/Makefile $VERSFILE" if [ "$LIBS" != "" ] then # tack on libraries, finding as we go for LIB in $LIBS do # strip off switch LIBNAME="${LIB#-[lsd]}" # look at linkage case "$LIB" in -l*|-s*) # force static load LIBPATH="$(find-lib $LIBNAME.a $LDIRS)" if [ "$LIBPATH" != "" ] then # add it to dependencies DEPS="$DEPS $LIBPATH" # convert to individual object files convert-static "$LIBPATH" || exit $? fi ;; esac done fi # produce static library echo $CMD $CMD || exit $? # remove temporaries rm -rf ld-tmp # produce dependencies if [ "$DEPFILE" != "" ] && [ "$DEPS" != "" ] then echo "$TARG: $DEPS" > "$DEPFILE" fi sra_sdk-2.1.7/build/ld.sh0000755001221300116200000001672011625212547014703 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # prepare script name SELF_NAME="$(basename $0)" BUILD_DIR="$(dirname $0)" TOP="$(dirname $BUILD_DIR)" SCRIPT_BASE="${0%.sh}" # os OS="$1" shift # architecture ARCH="$1" shift # binary loader tool LD="$1" shift # configuration unset SHLX unset DYLX unset LIBX unset OBJX unset LOBX # parameters TYPE=exe STATIC=0 DYLD=0 STATICSYSLIBS=0 CHECKSUM=0 THREADS=0 KPROC=0 unset BUILD unset LDIRS unset XDIRS unset SRCDIR unset BINDIR unset VERSFILE unset VERSDIR unset TARG unset EXT unset OBJS unset LIBS unset DEPFILE while [ $# -ne 0 ] do case "$1" in --build) BUILD="$2" shift ;; --ldflags) LDFLAGS="$2" shift ;; --static-system-libs) STATICSYSLIBS=1 ;; --checksum) CHECKSUM=1 ;; --shlx) SHLX="$2" shift ;; --dylx) SHLX="$2" shift ;; --libx) LIBX="$2" shift ;; --objx) OBJX="$2" shift ;; --srcdir) SRCDIR="$2" shift ;; --bindir) BINDIR="$2" shift ;; -MD) DEPFILE=1 ;; -L*) ARG="${1#-L}" if [ "$ARG" = "" ] then ARG="$2" shift fi LDIRS="$LDIRS:$ARG" ;; -X*) ARG="${1#-X}" if [ "$ARG" = "" ] then ARG="$2" shift fi XDIRS="$XDIRS:$ARG" ;; --dlib) TYPE=dlib ;; --slib) TYPE=slib ;; --stub) TYPE=stub ;; --exe) TYPE=exe ;; --static) STATIC=1 ;; --vers) if [ -f "$2" ] then VERSFILE="$2" elif [ -d "$2" ] then VERSDIR="$2" else echo "$SELF_NAME: expected version file or source directory" exit 3 fi shift ;; -o*) ARG="${1#-o}" if [ "$ARG" = "" ] then ARG="$2" shift fi TARG="$ARG" ;; -lpthread|-spthread|-dpthread) THREADS=8 ;; -lkproc) LIBS="$LIBS $1" KPROC=4 ;; -skproc) LIBS="$LIBS $1" THREADS=8 KPROC=4 ;; -l*|-s*) LIBS="$LIBS $1" ;; -dkproc) LIBS="$LIBS $1" KPROC=4 DYLD=2 ;; -d*) LIBS="$LIBS $1" DYLD=2 ;; *.$OBJX) OBJS="$OBJS $1" ;; esac shift done # correct for prefixes LDIRS="${LDIRS#:}" XDIRS="${XDIRS#:}" LIBS="${LIBS# }" OBJS="${OBJS# }" # split target OUTDIR=$(dirname "$TARG") NAME=$(basename "$TARG") # dependency file [ "$DEPFILE" != "" ] && DEPFILE="$NAME.$TYPE.d" # parse target if [ "$TYPE" = "dlib" ] && [ "$DYLX" != "" ] then EXT="$DYLX" NAME="${NAME%.$DYLX}" fi unset VERS if [ "$NAME" != "${NAME%.[0-9][0-9]*}" ] then ARG="${NAME%.[0-9][0-9]*}" VERS="${NAME#$ARG}" NAME="${ARG#.}" if [ "$NAME" != "${NAME%.[0-9][0-9]*}" ] then ARG="${NAME%.[0-9][0-9]*}" VERS="${NAME#$ARG}.$VERS" NAME="${ARG#.}" if [ "$NAME" != "${NAME%.[0-9][0-9]*}" ] then ARG="${NAME%.[0-9][0-9]*}" VERS="${NAME#$ARG}.$VERS" NAME="${ARG#.}" fi fi fi case "$TYPE" in dlib) if [ "$SHLX" != "" ] then EXT="$SHLX" NAME="${NAME%.$SHLX}" fi ;; slib) EXT="$LIBX" NAME="${NAME%.$LIBX}" esac unset DBGAP if [ "$NAME" != "${NAME%-dbgap}" ] then DBGAP=-dbgap NAME="${NAME%-dbgap}" fi # locate version file and version [ "$VERSDIR" != "" ] && VERSFILE="$VERSDIR/$NAME.vers" if [ "$VERSFILE" != "" ] then if [ ! -f "$VERSFILE" ] then echo "$SELF_NAME: warning - creating version file '$VERSFILE'" echo 1.0.0 > $VERSFILE fi if [ ! -r "$VERSFILE" ] then echo "$SELF_NAME: version file '$VERSFILE' is unreadable" exit 5 fi ARG=$(cat $VERSFILE) if [ "$VERS" != "" ] && [ "$VERS" != "$ARG" ] then echo "$SELF_NAME: version from file '$VERSFILE' does not match '$VERS'" exit 5 fi VERS="$ARG" fi #echo "# $SELF_NAME" #echo "# BUILD : $BUILD" #echo "# OS : $OS" #echo "# ARCH : $ARCH" #echo "# tool : $LD" #echo "# dep file : $DEPFILE" #echo "# LDFLAGS : $LDFLAGS" #echo "# static sys libs: $STATICSYSLIBS" #echo "# checksum : $CHECKSUM" #echo "# static : $STATIC" #echo "# kproc : $KPROC" #echo "# thread libs : $THREADS" #echo "# type : $TYPE" #echo "# srcdir : $SRCDIR" #echo "# bindir : $BINDIR" #echo "# LDIRS : $LDIRS" #echo "# XDIRS : $XDIRS" #echo "# vers file : $VERSFILE" #echo "# vers dir : $VERSDIR" #echo "# target : $TARG" #echo "# outdir : $OUTDIR" #echo "# name : $NAME" #echo "# dbgap : $DBGAP" #echo "# extension : $EXT" #echo "# version : $VERS" #echo "# objects : $OBJS" #echo "# libraries : $LIBS" #echo "# script-base : $SCRIPT_BASE" # overwrite dependencies [ -f "$DEPFILE" ] && rm -f "$DEPFILE" # generate mode [ $STATIC -ne 0 ] && [ $KPROC -ne 0 ] && THREADS=8 MODE=$(expr $THREADS + $KPROC + $DYLD + $STATIC) # generate SCM flags SCMFLAGS=$(expr $STATICSYSLIBS + $STATICSYSLIBS + $CHECKSUM) # perform link "$SCRIPT_BASE.$OS.$TYPE.sh" "$LD" "$ARCH" "$BUILD" "$SRCDIR" "$BINDIR" "$OUTDIR" \ "$TARG" "$NAME" "$DBGAP" "$VERS" "$VERSFILE" "$DEPFILE" "$MODE" "$SCMFLAGS" \ "$LDFLAGS" "$LDIRS" "$XDIRS" "$OBJS" "$LIBS" || exit $? # establish links if [ "$VERS" != "" ] && [ "$OS" != "win" ] then $SCRIPT_BASE.$OS.ln.sh "$TYPE" "$OUTDIR" "$TARG" "$NAME" "$DBGAP" "$EXT" "$VERS" fi # SCM if [ $CHECKSUM -eq 1 ] && [ "$OS" = "linux" ] then # calling the scm-version-script # parameters are: module-name, current-md5-file, version-file if [ $TYPE = "dlib" ] || [ $TYPE = "exe" ] || [ $STATIC -eq 1 ] then SCM_DIR="$TOP/scm" LOGFILE="$SCM_DIR/scm.log" SCMD="$BUILD_DIR/scm.sh $NAME $TARG.md5 $VERSFILE" echo "$SCMD" >> $LOGFILE $SCMD fi fi sra_sdk-2.1.7/build/ld.unix.cmn.sh0000755001221300116200000000577711556621243016453 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # script name SELF_NAME="$(basename $0)" # parameters LD="$1" shift SRCDIR="$1" OUTDIR="$2" TARG="$3" NAME="$4" DBGAP="$5" shift 5 VERS="$1" VERSFILE="$2" DEPFILE="$3" shift 3 MODE="$1" SCMFLAGS="$2" LDFLAGS="$3" shift 3 LDIRS="$1" XDIRS="$2" shift 2 OBJS="$1" LIBS="$2" # decode MODE STATIC=$(expr $MODE % 2) DYLD=$(expr $MODE / 2) # decode SCMFLAGS CHECKSUM=$(expr $SCMFLAGS % 2) STATICSYSLIBS=$(expr $SCMFLAGS / 2) # return parameter for find-lib LIBPATH='' # initial command state CMD='' LD_STATIC_STATE=0 LD_ALL_STATE=0 # for breaking out version set-vers () { MAJ=$1 MIN=$2 REL=$3 } # for locating libraries find-lib () { _lib="lib$1" _dirs="$2" LIBPATH='' while [ "$_dirs" != "" ] do _dir="${_dirs%%:*}" if [ "$_dir" != "" ] then if [ -e "$_dir/$_lib" ] then while [ -L "$_dir/$_lib" ] do _lib=$(stat -c '%N' "$_dir/$_lib" | tr "\`\'" " ") _lib="${_lib#*->}" _lib="lib${_lib# *lib}" _lib="${_lib%% *}" done LIBPATH="$_dir/$_lib" break; fi fi _dirs="${_dirs#$_dir}" _dirs="${_dirs#:}" done } # setting state load-static () { if [ $LD_STATIC_STATE -eq 0 ] then CMD="$CMD $LD_STATIC" LD_STATIC_STATE=1 fi } load-dynamic () { if [ $LD_STATIC_STATE -eq 1 ] then CMD="$CMD $LD_DYNAMIC" LD_STATIC_STATE=0 fi } load-all-symbols () { if [ $LD_ALL_STATE -eq 0 ] then CMD="$CMD $LD_ALL_SYMBOLS" LD_ALL_STATE=1 fi } load-ref-symbols () { if [ $LD_ALL_STATE -eq 1 ] then CMD="$CMD $LD_REF_SYMBOLS" LD_ALL_STATE=0 fi } sra_sdk-2.1.7/build/ld.unix.slib.sh0000755001221300116200000000620711506455277016623 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # =========================================================================== # input library types, and their handling # # normal or static linkage # -l : require static # -s : require static # -d : ignore # =========================================================================== # initialize command CMD="ar -rc" # function to convert an archive into individual object files convert-static () { # list members local path="$1" local mbrs="$(ar -t $path)" # unpack archive into temporary directory mkdir -p ld-tmp if ! cd ld-tmp then echo "$SELF_NAME: failed to cd to ld-tmp" exit 5 fi ar -x "$path" # rename and add to source files list local m= for m in $mbrs do mv $m $NAME-$m CMD="$CMD ld-tmp/$NAME-$m" done # return to prior location cd - > /dev/null } # versioned output if [ "$VERS" = "" ] then CMD="$CMD $TARG" else set-vers $(echo $VERS | tr '.' ' ') CMD="$CMD $OUTDIR/$NAME$DBGAP.a.$VERS" fi # tack on object files CMD="$CMD $OBJS" # initial dependency upon Makefile and vers file DEPS="$SRCDIR/Makefile $VERSFILE" if [ "$LIBS" != "" ] then # tack on libraries, finding as we go for LIB in $LIBS do # strip off switch LIBNAME="${LIB#-[lsd]}" # look at linkage case "$LIB" in -l*|-s*) # force static load LIBPATH="$(find-lib $LIBNAME.a $LDIRS)" if [ "$LIBPATH" != "" ] then # add it to dependencies DEPS="$DEPS $LIBPATH" # convert to individual object files convert-static "$LIBPATH" || exit $? fi ;; esac done fi # produce static library echo $CMD $CMD || exit $? # remove temporaries rm -rf ld-tmp # produce dependencies if [ "$DEPFILE" != "" ] && [ "$DEPS" != "" ] then echo "$TARG: $DEPS" > "$DEPFILE" fi sra_sdk-2.1.7/build/ld.win.cmn.sh0000755001221300116200000000565711625212550016254 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # script name SELF_NAME="$(basename $0)" # parameters LD="$1" ARCH="$2" BUILD="$3" shift 3 SRCDIR="$1" BINDIR="$2" OUTDIR="$3" TARG="$4" NAME="$5" DBGAP="$6" shift 6 VERS="$1" VERSFILE="$2" DEPFILE="$3" shift 3 MODE="$1" SCMFLAGS="$2" LDFLAGS="$3" shift 3 LDIRS="$1" XDIRS="$2" shift 2 OBJS="$1" LIBS="$2" # decode MODE STATIC=$(expr $MODE % 2) MODE=$(expr $MODE / 2) DYLD=$(expr $MODE % 2) MODE=$(expr $MODE / 2) KPROC=$(expr $MODE % 2) THREADS=$(expr $MODE / 2) ##### TEMPORARY ##### KPROC=0 THREADS=0 ##################### # decode SCMFLAGS CHECKSUM=$(expr $SCMFLAGS % 2) STATICSYSLIBS=$(expr $SCMFLAGS / 2) # return parameter for find-lib xLIBPATH='' # initial command state CMD='' LD_STATIC_STATE=0 LD_ALL_STATE=0 # for breaking out version set-vers () { MAJ=$1 MIN=$2 REL=$3 } # for locating libraries find-lib () { _lib="lib$1" _dirs="$2" xLIBPATH='' while [ "$_dirs" != "" ] do _dir="${_dirs%%:*}" if [ "$_dir" != "" ] then if [ -e "$_dir/$_lib" ] then xLIBPATH="$_dir/$_lib" break; fi fi _dirs="${_dirs#$_dir}" _dirs="${_dirs#:}" done } # setting state load-static () { if [ $LD_STATIC_STATE -eq 0 ] then CMD="$CMD $LD_STATIC" LD_STATIC_STATE=1 fi } load-dynamic () { if [ $LD_STATIC_STATE -eq 1 ] then CMD="$CMD $LD_DYNAMIC" LD_STATIC_STATE=0 fi } load-all-symbols () { if [ $LD_ALL_STATE -eq 0 ] then CMD="$CMD $LD_ALL_SYMBOLS" LD_ALL_STATE=1 fi } load-ref-symbols () { if [ $LD_ALL_STATE -eq 1 ] then CMD="$CMD $LD_REF_SYMBOLS" LD_ALL_STATE=0 fi } sra_sdk-2.1.7/build/ld.win.exe.sh0000755001221300116200000001713111625212550016246 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # =========================================================================== # input library types, and their handling # # normal linkage # -l : find shared or static # -s : require static # -d : ignore - will be dynamically loaded # # static linkage # -l : require static # -s : require static # -d : require static # =========================================================================== # script name SELF_NAME="$(basename $0)" # parameters and common functions source "${0%exe.sh}cmn.sh" # discover tool chain case "$LD" in link) source "${0%exe.sh}vc++.sh" ;; *) echo "$SELF_NAME: unrecognized ld tool - '$LD'" exit 5 esac # EXE_CMD was started in tool-specific source CMD="$EXE_CMD $LDFLAGS OLE32.lib" # if building a static executable against dynamic libraries # the main application will substitute for name lookup if [ $STATIC -eq 1 ] && [ $DYLD -eq 1 ] then CMD="$CMD $LD_EXPORT_GLOBAL $LD_MULTIPLE_DEFS" fi # function to convert static libraries to individual COFF files convert-static () { if [ $STATIC -eq 0 ] then CMD="$CMD $2.a" else # list members local path="$1" local mbrs="$(ar -t $path)" # create sub directory rm -rf "$2" && mkdir "$2" if ! cd "$2" then echo "$SELF_NAME: failed to cd to $2" exit 5 fi ar -x "$path" # add source files to link local m= for m in $mbrs do CMD="$CMD $2/$m" done # return to prior location cd - > /dev/null fi } # tack on object files CMD="$CMD $(cygpath -w $OBJS)" # initial dependency upon Makefile - no vers file on Windows DEPS="$SRCDIR/Makefile" if [ "$LIBS" != "" ] then # tack on paths DIRS="$LDIRS:$XDIRS" while [ "$DIRS" != "" ] do DIR="${DIRS%%:*}" [ "$DIR" != "" ] && CMD="$CMD /LIBPATH:$(cygpath -w $DIR)" DIRS="${DIRS#$DIR}" DIRS="${DIRS#:}" done HAVE_KERNEL32=0 HAVE_WS2=0 HAVE_CLIB=0 if [ $THREADS -ne 0 ] || [ $KPROC -ne 0 ] then if [ $STATIC -ne 0 ] then CMD="$CMD /MT" else CMD="$CMD /MD" fi fi # tack on libraries, finding as we go for xLIB in $LIBS do # strip off switch xLIBNAME="${xLIB#-[lsd]}" # map xLIBNAME case "$xLIBNAME" in dl) if [ $HAVE_KERNEL32 -ne 1 ] then load-ref-symbols load-dynamic CMD="$CMD Kernel32.lib" HAVE_KERNEL32=1 fi continue ;; ws2) if [ $HAVE_WS2 -ne 1 ] then load-ref-symbols load-dynamic CMD="$CMD ws2_32.lib" HAVE_WS2=1 fi continue ;; # redirect libm to link against libc.lib in case of windows # omitting the lib defaults to linking against libc.lib m) if [ $HAVE_CLIB -ne 1 ] then load-ref-symbols load-dynamic HAVE_CLIB=1 fi continue ;; ##### TEMPORARY ##### # skip kproc kproc) continue ;; ##################### esac # look at linkage case "$xLIB" in -l*) # normal or dynamic linkage FOUND=0 if [ $STATIC -eq 0 ] then find-lib $xLIBNAME.lib $LDIRS if [ "$xLIBPATH" != "" ] then # found it FOUND=1 # load dynamic load-dynamic CMD="$CMD lib$xLIBNAME.lib" fi fi # try static only if [ $FOUND -eq 0 ] then find-lib $xLIBNAME.a $LDIRS if [ "$xLIBPATH" != "" ] then # found it FOUND=1 # add it to dependencies DEPS="$DEPS $xLIBPATH" # load static load-static [ $STATIC -eq 1 ] && load-all-symbols convert-static "$xLIBPATH" "lib$xLIBNAME" fi fi # not found within our directories if [ $FOUND -eq 0 ] then [ $STATIC -eq 1 ] && load-ref-symbols load-dynamic CMD="$CMD lib$xLIBNAME.lib" fi ;; -s*) # force static load FOUND=0 find-lib $xLIBNAME.a $LDIRS if [ "$xLIBPATH" != "" ] then # found it FOUND=1 # add it to dependencies DEPS="$DEPS $xLIBPATH" # load static load-static [ $STATIC -eq 1 ] && load-all-symbols convert-static "$xLIBPATH" "lib$xLIBNAME" fi # not found within our directories if [ $FOUND -eq 0 ] then # set load to static load-static [ $STATIC -eq 1 ] && load-all-symbols CMD="$CMD lib$xLIBNAME.lib" fi ;; -d*) FOUND=0 if [ $STATIC -eq 1 ] then find-lib $xLIBNAME.a $LDIRS if [ "$xLIBPATH" != "" ] then # found it FOUND=1 # add it to dependencies DEPS="$DEPS $xLIBPATH" # load static load-static load-all-symbols convert-static "$xLIBPATH" "lib$xLIBNAME" fi # not found within our directories if [ $FOUND -eq 0 ] then load-static load-all-symbols CMD="$CMD lib$xLIBNAME" fi fi ;; esac done fi # return to normal load-ref-symbols load-dynamic # produce shared library echo $CMD $CMD || exit $? # produce dependencies if [ "$DEPFILE" != "" ] then echo "$TARG: $DEPS" > "$DEPFILE" fi # cleanup temporary files rm -f $TARG.lib $TARG.exp sra_sdk-2.1.7/build/ld.win.slib.sh0000755001221300116200000000673211506455277016440 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # =========================================================================== # input library types, and their handling # # normal or static linkage # -l : require static # -s : require static # -d : ignore # =========================================================================== # script name SELF_NAME="$(basename $0)" # parameters and common functions source "${0%slib.sh}cmn.sh" # initialize command if [ $STATIC -eq 0 ] then CMD="lib /NOLOGO" else CMD="ar -rc" fi # function to convert an archive into individual object files convert-static () { if [ $STATIC -eq 0 ] then CMD="$CMD $(cygpath -w $1)" else # list members local path="$1" local mbrs="$(ar -t $path)" # unpack archive into temporary directory mkdir -p ld-tmp if ! cd ld-tmp then echo "$SELF_NAME: failed to cd to ld-tmp" exit 5 fi ar -x "$path" # rename and add to source files list local m= for m in $mbrs do mv $m $NAME-$m CMD="$CMD ld-tmp/$NAME-$m" done # return to prior location cd - > /dev/null fi } if [ $STATIC -eq 0 ] then # no versioned output here, sorry CMD="$CMD /OUT:$(cygpath -w $TARG)" # tack on object files CMD="$CMD $(cygpath -w $OBJS)" else CMD="$CMD $TARG $OBJS" fi # initial dependency upon Makefile and vers file DEPS="$SRCDIR/Makefile" if [ "$LIBS" != "" ] then # tack on libraries, finding as we go for xLIB in $LIBS do # strip off switch xLIBNAME="${xLIB#-[lsd]}" # look at linkage case "$xLIB" in -l*|-s*) # force static load xLIBPATH="$(find-lib $xLIBNAME.lib $LDIRS)" if [ "$xLIBPATH" != "" ] then # add it to dependencies DEPS="$DEPS $xLIBPATH" # convert to individual object files convert-static "$xLIBPATH" || exit $? fi ;; esac done fi # produce static library echo $CMD $CMD || exit $? # remove temporaries rm -rf ld-tmp # produce dependencies if [ "$DEPFILE" != "" ] && [ "$DEPS" != "" ] then echo "$TARG: $DEPS" > "$DEPFILE" fi sra_sdk-2.1.7/build/ld.win.stub.sh0000755001221300116200000000363711506455277016465 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # =========================================================================== # input library types, and their handling # # normal linkage # -l : find shared or static # -s : require static # -d : require shared # # static linkage # -l : require static # -s : require static # -d : ignore # =========================================================================== # script name SELF_NAME="$(basename $0)" # parameters and common functions source "${0%stub.sh}cmn.sh" # discover tool chain case "$LD" in link) source "${0%stub.sh}vc++.sh" ;; *) echo "$SELF_NAME: unrecognized ld tool - '$LD'" exit 5 esac # produce stub library and exp file echo $STUB_CMD $STUB_CMD sra_sdk-2.1.7/build/ld.win.vc++.sh0000755001221300116200000000443311506455277016241 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # define linker params LD_EXPORT_GLOBAL="" LD_MULTIPLE_DEFS="/FORCE:MULTIPLE" LD_STATIC="" LD_DYNAMIC="" LD_ALL_SYMBOLS="/OPT:NOREF" LD_REF_SYMBOLS="/OPT:REF" # rewrite PATH variable unset CYGP while [ "$PATH" = "${PATH#/cygdrive}" ] do DIR="${PATH%%:*}" PATH="${PATH#$DIR}" PATH="${PATH#:}" CYGP="$CYGP:$DIR" done PATH="$PATH$CYGP" export PATH # the def file unset DEF_SWITCH DEF_FILE="$SRCDIR/$NAME-$BUILD.def" [ ! -f "$DEF_FILE" ] && DEF_FILE="$SRCDIR/$NAME.def" [ -f "$DEF_FILE" ] && DEF_SWITCH="/DEF:$(cygpath -w $DEF_FILE)" || unset DEF_FILE # the full path to target sans extension WINTARG="$(cygpath -w ${TARG%.lib})" # build command STUB_CMD="lib /NOLOGO /MACHINE:x86 $DEF_SWITCH /OUT:$WINTARG.lib" DLIB_CMD="$LD /NOLOGO /DLL $DEF_SWITCH /OUT:$WINTARG.dll /STACK:8000000 /HEAP:1000000000" EXE_CMD="$LD /NOLOGO /OUT:$WINTARG.exe /SUBSYSTEM:CONSOLE /ENTRY:wmainCRTStartup /STACK:8000000 /HEAP:100000000" # tack on PDB tracking if [ "$BUILD" = "dbg" ] then DLIB_CMD="$DLIB_CMD /DEBUG /PDB:$WINTARG.pdb" EXE_CMD="$EXE_CMD /DEBUG /PDB:$WINTARG.pdb" fi sra_sdk-2.1.7/build/sra-dflt-schema.sh0000755001221300116200000000474711506455277017273 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # prepare script name SELF_NAME="$(basename $0)" SCRIPT_BASE="${0%.sh}" # os OS="$1" shift # binary compiler CC="$1" shift # everything except windows is fine as-is if [ "$OS" != "win" ] then echo "$CC $*" $CC $* exit $? fi # state unset ARGS unset DEPENDENCIES unset DEPTARG unset TARG # process parameters for windows while [ $# -ne 0 ] do case "$1" in -o*) ARG="${1#-o}" if [ "$ARG" = "" ] then ARG="$2" shift fi TARG="$ARG" ARG="$(cygpath -w $ARG)" ARGS="$ARGS -o$ARG" ;; -I*) ARG="${1#-I}" if [ "$ARG" = "" ] then ARG="$2" shift fi ARG="$(cygpath -w $ARG)" ARGS="$ARGS -I$ARG" ;; -T*) ARG="${1#-T}" if [ "$ARG" = "" ] then ARG="$2" shift fi DEPTARG="$ARG" DEPENDENCIES=1 ARG="$(cygpath -w $ARG)" ARGS="$ARGS -T$ARG" ;; *) ARG="$(cygpath -w $1)" ARGS="$ARGS $ARG" ;; esac shift done echo "$CC $ARGS" if ! $CC $ARGS then STATUS=$? rm -f $TARG $DEPTARG exit $? fi if [ $DEPENDENCIES -eq 1 ] then # fix this rm -f $DEPTARG fi sra_sdk-2.1.7/build/win-cc.sh0000755001221300116200000000677611542737113015475 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # prepare script name SELF_NAME="$(basename $0)" SCRIPT_BASE="${0%.sh}" # os OS="$1" shift # binary compiler CC="$1" shift # configuration unset TARG unset ARGS unset OBJX unset SRCFILE unset SOURCES unset DEPENDENCIES while [ $# -ne 0 ] do case "$1" in --cflags) for ARG in $2 do [ "$ARG" != "${ARG#-}" ] && ARG="/${ARG#-}" ARGS="$ARGS $ARG" done shift ;; --checksum) ;; --objx) OBJX="$2" shift ;; -D*) ARG="${1#-D}" if [ "$ARG" = "" ] then ARG="$2" shift fi ARGS="$ARGS /D$ARG" ;; -I*) ARG="${1#-I}" if [ "$ARG" = "" ] then ARG="$2" shift fi ARG="$(cygpath -w $ARG)" ARGS="$ARGS /I$ARG" ;; -o*) ARG="${1#-o}" if [ "$ARG" = "" ] then ARG="$2" shift fi ARGS="$ARGS /Fo$ARG" TARG="${ARG%.$OBJX}" ;; -MD) # the /showIncludes switch will generate # includes to stderr, but they will need # to be filtered out and rewritten to the *.d ARGS="$ARGS /showIncludes" DEPENDENCIES=1 ;; -fPIC|-std=c99|-ansi|-pedantic) ;; -*) ARG="/${1#-}" ARGS="$ARGS $ARG" ;; *) SRCFILE="$(basename $1)" SOURCES="$SOURCES $1" ARG="$(cygpath -w $1)" ARGS="$ARGS $ARG" ;; esac shift done unset STATUS CMD="$CC $ARGS" echo "$CMD" # run command with redirection if $CMD > $TARG.out 2> $TARG.err then # success STATUS=0 else # failure STATUS=$? fi # check for dependencies if [ "$DEPENDENCIES" = "1" ] then sed -e '/including file/!d' -e 's/.*including file: *\([^\r\n][^\r\n]*\)/\1/g' -e '/ /d' $TARG.out > $TARG.inc echo -n "$TARG.$OBJX: $SOURCES" | sed -e 's/\r//g' > $TARG.d for inc in $(cat $TARG.inc) do echo -n " $(cygpath -u $inc)" | sed -e 's/\r//g' >> $TARG.d done fi # repeat output files but without CR sed -e 's/\r//g' $TARG.err > /dev/stderr sed -e 's/\r//g' -e "/^$SRCFILE$/d" -e '/including file/d' $TARG.out # clean up files rm -f $TARG.out $TARG.err $TARG.inc exit $STATUS sra_sdk-2.1.7/build/mac.arch.sh0000755001221300116200000000465111645105470015756 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # PPC or Intel? ARCH="$(uname -m)" # the Mac likes to keep its architecture hidden because for all practical # purposes, it is both 32 and 64 bit, and makes use of emulation as needed. # does the hardware support 64-bit mode, even in emulation? CAP64=$(/usr/sbin/sysctl -n hw.cpu64bit_capable) # real 64-bit hardware has > 32 bits of address space PADDR_BITS=$(/usr/sbin/sysctl -n machdep.cpu.address_bits.physical) VADDR_BITS=$(/usr/sbin/sysctl -n machdep.cpu.address_bits.virtual) # to be 64-bit, it's probably sufficient to test the address space # but we have the emulation information as well. if [ $CAP64 -ne 0 ] then if [ $PADDR_BITS -gt 32 ] && [ $VADDR_BITS -gt 32 ] then # call it 64-bit if [ "$ARCH" = "i386" ] || [ "$ARCH" = "x86_64" ] then echo "x86_64" exit 0 fi if [ "$ARCH" = "Power Macintosh" ] then echo "ppc64" exit 0 fi # unrecognized echo "unrecognized" exit 5 fi fi # call it 32-bit if [ "$ARCH" = "i386" ] then echo "i386" exit 0 fi if [ "$ARCH" = "Power Macintosh" ] then echo "ppc32" exit 0 fi # unrecognized echo "unrecognized" exit 5 sra_sdk-2.1.7/build/ld.win.dlib.sh0000755001221300116200000002000411625212550016370 0ustar rodarmertrace#!/bin/bash # =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # =========================================================================== # input library types, and their handling # # normal linkage # -l : find shared or static # -s : require static # -d : require shared # # static linkage # -l : require static # -s : require static # -d : ignore # =========================================================================== # script name SELF_NAME="$(basename $0)" # parameters and common functions source "${0%dlib.sh}cmn.sh" # discover tool chain case "$LD" in link) source "${0%dlib.sh}vc++.sh" ;; *) echo "$SELF_NAME: unrecognized ld tool - '$LD'" exit 5 esac # DLIB_CMD was started in tool-specific source CMD="$DLIB_CMD $LDFLAGS OLE32.lib" # function to convert static libraries to individual COFF files convert-static () { if [ $STATIC -eq 0 ] then CMD="$CMD $2.a" else # list members local path="$1" local mbrs="$(ar -t $path)" # create sub directory rm -rf "$2" && mkdir "$2" if ! cd "$2" then echo "$SELF_NAME: failed to cd to $2" exit 5 fi ar -x "$path" # add source files to link local m= for m in $mbrs do CMD="$CMD $2/$m" done # return to prior location cd - > /dev/null fi } # tack on object files CMD="$CMD $(cygpath -w $OBJS)" # initial dependency upon Makefile and vers file DEPS="$SRCDIR/Makefile $DEF_FILE" if [ "$LIBS" != "" ] then # tack on paths DIRS="$LDIRS:$XDIRS" while [ "$DIRS" != "" ] do DIR="${DIRS%%:*}" [ "$DIR" != "" ] && CMD="$CMD /LIBPATH:$(cygpath -w $DIR)" DIRS="${DIRS#$DIR}" DIRS="${DIRS#:}" done HAVE_KERNEL32=0 HAVE_CLIB=0 if [ $THREADS -ne 0 ] || [ $KPROC -ne 0 ] then [ $STATIC -eq 0 ] && CMD="$CMD /MD" fi # tack on libraries, finding as we go for xLIB in $LIBS do # strip off switch xLIBNAME="${xLIB#-[lsd]}" # map xLIBNAME case "$xLIBNAME" in # redirect libdl to link against Kernel32.lib in case of windows dl) if [ $HAVE_KERNEL32 -ne 1 ] then load-ref-symbols load-dynamic CMD="$CMD Kernel32.lib" HAVE_KERNEL32=1 fi continue ;; # redirect libm to link against libc.lib in case of windows # omitting the lib defaults to linking against libc.lib m) if [ $HAVE_CLIB -ne 1 ] then load-ref-symbols load-dynamic HAVE_CLIB=1 fi continue ;; ##### TEMPORARY ##### # skip kproc kproc) continue ;; ##################### esac # look at linkage case "$xLIB" in -l*) # normal or dynamic linkage FOUND=0 if [ $STATIC -eq 0 ] then find-lib $xLIBNAME.lib $LDIRS if [ "$xLIBPATH" != "" ] then # found it FOUND=1 # load normally load-ref-symbols load-dynamic CMD="$CMD lib$xLIBNAME.lib" fi fi # try static only if [ $FOUND -eq 0 ] then find-lib $xLIBNAME.a $LDIRS if [ "$xLIBPATH" != "" ] then # found it FOUND=1 # add it to dependencies DEPS="$DEPS $xLIBPATH" # load static load-static load-all-symbols convert-static "$xLIBPATH" "lib$xLIBNAME" fi fi # not found within our directories if [ $FOUND -eq 0 ] then # set load to normal load-ref-symbols load-dynamic CMD="$CMD lib$xLIBNAME.lib" fi ;; -s*) # force static load FOUND=0 find-lib $xLIBNAME.a $LDIRS if [ "$xLIBPATH" != "" ] then # found it FOUND=1 # add it to dependencies DEPS="$DEPS $xLIBPATH" # load static load-static load-all-symbols convert-static "$xLIBPATH" "lib$xLIBNAME" fi # not found within our directories if [ $FOUND -eq 0 ] then # set load to static load-static load-all-symbols CMD="$CMD lib$xLIBNAME.lib" fi ;; -d*) # only dynamic linkage FOUND=0 if [ $STATIC -eq 0 ] then find-lib $xLIBNAME.lib $LDIRS if [ "$xLIBPATH" != "" ] then # found it FOUND=1 # load normally load-ref-symbols load-dynamic CMD="$CMD lib$xLIBNAME.lib" fi fi # try static if performing static build # because we HAVE to link against something, # and the dependency code is being statically # linked into an executable... if [ $FOUND -eq 0 ] && [ $STATIC -eq 1 ] then find-lib $xLIBNAME.a $LDIRS if [ "$xLIBPATH" != "" ] then # found it FOUND=1 # add it to dependencies DEPS="$DEPS $xLIBPATH" # load static load-static load-all-symbols convert-static "$xLIBPATH" "lib$xLIBNAME" fi fi # not found within our directories if [ $FOUND -eq 0 ] then # set load to normal load-ref-symbols load-dynamic CMD="$CMD lib$xLIBNAME.lib" fi ;; esac done fi # put state back to normal load-ref-symbols load-dynamic # produce shared library, stub library and exp file echo $CMD if ! $CMD then STATUS=$? rm -f "$TARG" "${TARG%lib}dll" exit $STATUS fi # copy dll to binary directory, so they can be found by the executables # leave the dll in it's original place, so that they can be found in /mod and /wmod too cp "${TARG%lib}dll" "$BINDIR" # produce dependencies if [ "$DEPFILE" != "" ] then echo "$TARG: $DEPS" > "$DEPFILE" fi sra_sdk-2.1.7/build/Makefile.mac0000644001221300116200000000363511476747337016163 0ustar rodarmertrace# =========================================================================== # # PUBLIC DOMAIN NOTICE # National Center for Biotechnology Information # # This software/database is a "United States Government Work" under the # terms of the United States Copyright Act. It was written as part of # the author's official duties as a United States Government employee and # thus cannot be copyrighted. This software/database is freely available # to the public for use. The National Library of Medicine and the U.S. # Government have not placed any restriction on its use or reproduction. # # Although all reasonable efforts have been taken to ensure the accuracy # and reliability of the software and data, the NLM and the U.S. # Government do not and cannot warrant the performance or results that # may be obtained by using this software or data. The NLM and the U.S. # Government disclaim all warranties, express or implied, including # warranties of performance, merchantability or fitness for any particular # purpose. # # Please cite the author in any work or product based on this material. # # =========================================================================== # default compiler ifeq (,$(COMP)) COMP = gcc endif # architecture xARCH = $(shell test -f $(TOP)/build/ARCH.mac && cat $(TOP)/build/ARCH.mac) ifneq (,$(xARCH)) # the user has selected an architecture ifeq (i386,$(xARCH)) ARCH = i386 BITS = 32 endif ifeq (x86_64,$(xARCH)) ARCH = x86_64 BITS = 64 endif endif # allow the user to override architecture i386 x86_64: @ echo $@ > $(TOP)/build/ARCH.mac .PHONY: i386 x86_64 # library prefix LPFX = lib # file extensions OBJX = o LOBX = pic.o LIBX = a SHLX = dylib # compilation defines DEFINES := -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 # Darwin is a Unix variant OS_DAD = bsd OS_GDAD = unix LIBXML_LPATH = /usr/lib sra_sdk-2.1.7/build/COMP.mac0000644001221300116200000000000411477732762015164 0ustar rodarmertracegcc sra_sdk-2.1.7/build/BUILD.win0000644001221300116200000000000411625267705015315 0ustar rodarmertracepub sra_sdk-2.1.7/build/COMP.win0000644001221300116200000000000511477733000015204 0ustar rodarmertracevc++ sra_sdk-2.1.7/doc/0000775001221300116200000000000011477730356013417 5ustar rodarmertracesra_sdk-2.1.7/doc/help/0000755001221300116200000000000011477730356014345 5ustar rodarmertracesra_sdk-2.1.7/doc/help/html/0000755001221300116200000000000011477730356015311 5ustar rodarmertracesra_sdk-2.1.7/doc/help/html/abi-dump-help.html0000644001221300116200000000371711627507276020633 0ustar rodarmertrace abi-dump help 
Usage:
  abi-dump [options] [ -A ] <accession>
  abi-dump [options] <path>

  -A|--accession <accession>       Replaces accession derived from <path> in filename(s) and deflines

Options:

  -O|--outdir <path>               Output directory, default is '.'
  -N|--minSpotId <rowid>           Minimum spot id
  -X|--maxSpotId <rowid>           Maximum spot id
  -G|--spot-group                  Split into files by SPOT_GROUP (member name)
  --spot-groups <[list]>           Filter by SPOT_GROUP (member): name[,...]
  -R|--read-filter <[filter]>      Split into files by READ_FILTER value
                                   optionally filter by a value: pass|reject|criteria|redacted
  -T|--group-in-dirs               Split into subdirectories instead of files
  -K|--keep-empty-files            Do not delete empty files
  --table <table-name>             (New) Table name within SRA format, default is SEQUENCE

  -h|--help                        Output a brief explantion for the program
  -V|--version                     Display the version of the program then quit
  -L|--log-level <level>           Logging level as number or enum string
                                   One of (fatal|sys|int|err|warn|info) or (0-5)
                                   Current/default is warn
  -v|--verbose                     Increase the verbosity level of the program
                                   Use multiple times for more verbosity

Format options:

  -M|--minReadLen <len>            Minimum read length to output, default is 25
  -W|--noclip                      Do not clip quality left and right for spot
  -F|--origfmt                     Excludes SRR accession on defline
  -B|--noDotReads                  Do not output reads consisting mostly of dots
sra_sdk-2.1.7/doc/help/html/abi-load-help.html0000644001221300116200000000353111627507276020577 0ustar rodarmertrace abi-load help 
Usage:
  abi-load [options] -r run.xml -e experiment.xml -o output-path

  -r|--run-xml                     path to run.xml describing input files
  -e|--experiment                  path to experiment.xml
  -o|--output-path                 target location

Options:
  -i|--input-path                  input files location, default '.'
  -u|--input-unpacked              input files are unpacked
  -f|--force                       force target overwrite
  -n|--spots-number                process only given number of spots from input
  -b|--bad-spot-number             acceptable number of spot creation errors, default is 50
  -p|--bad-spot-percentage         acceptable percentage of spots creation errors, default is 5
  -x|--expected                    path to expected.xml
  -z|--xml-log                     produce XML-formatted log file
  -s|--intensities                 [on | off] load intensity data, default is off:
                                     Illumina: signal, intensity, noise;
                                     AB SOLiD: signal(s);
                                     LS454: signal, position (for SFF files ON by default).

  -h|--help                        Output a brief explantion for the program.
  -V|--version                     Display the version of the program then quit.
  -L|--log-level <level>           Logging level as number or enum string.
                                   One of (fatal|sys|int|err|warn|info) or (0-5)
                                   Current/default is warn
  -v|--verbose                     Increase the verbosity level of the program.
                                   Use multiple times for more verbosity.
sra_sdk-2.1.7/doc/help/html/bam-loader-help.html0000644001221300116200000000176211476747102021132 0ustar rodarmertrace bam-loader help 
Usage:
 bam-loader 0.0.1

bam-loader [Options] BAMFILE
    Load a bam file.

Options:
  -o, --output=TABLEPATH    REQUIRED: path to a table where the table will be put
  -V, --version             this will cause the program to emit the internal
                            version number before any other action
  -v, --verbose             extra information will be output during
                            processing second occurrence on the command line
                            means even more
  -h, -?, --help            print this message
  -l, --log-level=LEVEL     the next token will affect the logging level of
                            the program  accepted tokens are the numbers
                            0-15, fatal, sys, int, err, warn, info
                          , debug1...debug10
sra_sdk-2.1.7/doc/help/html/copycat-help.html0000644001221300116200000000472311476747102020571 0ustar rodarmertrace copycat help 
copycat : 1.0.6

Usage: 
    copycat [  ] src-file dst-file
    copycat [  ] src-file [src-file...] dst-dir
    copycat [  ] -o dst-dir src-file [src-file...]

    options:
      -x cache-dir         location to output cached files
      -f                   force overwrite of existing files
      -m magicfile         path to the magic file to use
      -e extfile           path to the extensions file to use
      -c classfile         path to the file class/type file

    behavior is intended to mimic 'cp' to a large extent, in that
    a single source file may be copied to a new name, or multiple
    source files may be copied to a destination directory.

    when the destination directory is specified using 'cp' semantics,
    the directory must exist. if specified via '-o' switch, it will be
    created if necessary.

    the target file may also be a device. in the special case of
    /dev/null, it may also act as a directory.

    the '-x' option allows small files that are typed as eligible for
    caching to be copied to the cache directory provided. the directory
    will be created if necessary.
    the intent is to capture top-level files, such that files are copied
    into the flat cache directory without regard to where they were found
    in the input hierarchy. in the case of name conflict, output files will
    be renamed.

    the class file, magic file and extension file allow new understandings
    of files found while cataloging
    the magic file is of the type used by the unix/linux 'file' command
    the class file assigns file type to classes
    the extension file assigns file extensions to file types

    existing classes are 'Archive', 'Cached', 'Compressed', 'Read'
    Archive and Compresses files are those that have contents that can
    be examined - new types must be compiled in
    Cached files are those affected by the -x option
    Read files are not handled seperately by copy cat except in the catalog
    new classes would like Read only be added to the catalog with the class

    the format for the class file is lines such as the below
        'GnuZipCompressed' with tabs and linefeeds

    the format for the extension file is lines such as the below
        'gzCompressed' with tabs and linefeeds
sra_sdk-2.1.7/doc/help/html/crc32sum-help.html0000644001221300116200000000053211476747102020562 0ustar rodarmertrace crc32 help 
: usage: crc32sum [
sra_sdk-2.1.7/doc/help/html/fastq-dump-help.html0000644001221300116200000001136611627507276021215 0ustar rodarmertrace fastq-dump help 
Usage:
  fastq-dump [options] [ -A ] <accession>
  fastq-dump [options] <path>

INPUT
  -A|--accession <accession>       Replaces accession derived from <path> in filename(s) and deflines
  --table <table-name>             (New) Table name within SRA format, default is SEQUENCE

PROCESSING

Read Splitting                     Sequence data may be used as raw or split into individual reads
  --split-spot                     Split spots into individual reads

Full Spot Filters                  Applied to the full spot independently of --split-spot
  -N|--minSpotId <rowid>           Minimum spot id
  -X|--maxSpotId <rowid>           Maximum spot id
  --spot-groups <[list]>           Filter by SPOT_GROUP (member): name[,...]
  -W|--clip                        Apply left and right clips

Common Filters                     Applied to spots when --split-spot is not set, otherwise - to individual reads
  -M|--minReadLen <len>            Filter by sequence length >= <len>
  -R|--read-filter <[filter]>      Split into files by READ_FILTER value
                                   optionally filter by a value: pass|reject|criteria|redacted
  -E|--qual-filter                 Filter used in early 1K Genomes data:
                                   no sequences starting or ending with >= 10N

Filters for individual reads       Applied only with --split-spot set
  --skip-technical                 Dump only biological reads

OUTPUT
  -O|--outdir <path>               Output directory, default is '.'

Multiple File Options              Setting this options will produce more than 1 file, which will be suffixed by splitting criteria.
  --split-files                    Dump each read into a separate file.Files will received suffix corresponding to read number
  --split-3                        Legacy 3-file splitting for mate-pairs:
                                   First 2 biological reads satisfying dumping conditions
                                   are placed in files *_1.fastq and *_2.fastq
                                   If only 1 biological read is dumpable - it is placed in *.fastq
                                   Biological reads 3 and above are ignored.
  -G|--spot-group                  Split into files by SPOT_GROUP (member name)
  -R|--read-filter <[filter]>      Split into files by READ_FILTER value
                                   optionally filter by a value: pass|reject|criteria|redacted
  -T|--group-in-dirs               Split into subdirectories instead of files
  -K|--keep-empty-files            Do not delete empty files

FORMATTING

Sequence
  -C|--dumpcs <[cskey]>            Formats sequence in color space (default for SOLiD),cskey may be specified for translation
  -B|--dumpbase                    Formats sequence in base sequence (default for other than SOLiD).

Quality
  -Q|--offset <integer>            Offset to use for quality conversion, default is 33
  --fasta                          Fasta only, no qualities

Defline
  -F|--origfmt                     Defline contains only original sequence name
  -I|--readids                     Append read id after spot id as 'accession.spot.readid' on defline
  --helicos                        Helicos style defline
  --defline-seq <fmt>              Defline format specification for sequence.
  --defline-qual <fmt>             Defline format specification for quailty.
                                   <fmt> is string of characters and/or variables. Variables could be are one of:
                                      $ac - accession, $si - spot id, $sn - spot name, $sg - spot group (barcode),
                                      $sl - spot length in bases, $ri - read number, $rn - read name, $rl - read length in bases.
                                   '[]' could be used for an optional output: if all vars in [] yield empty values whole group is not printed.
                                   Empty value is empty string or 0 for numeric variables.
                                   Ex: @$sn[_$rn]/$ri - '_$rn' is omitted if name is empty

OTHER:
  -h|--help                        Output a brief explantion for the program
  -V|--version                     Display the version of the program then quit
  -L|--log-level <level>           Logging level as number or enum string
                                   One of (fatal|sys|int|err|warn|info) or (0-5)
                                   Current/default is warn
  -v|--verbose                     Increase the verbosity level of the program
                                   Use multiple times for more verbosity
sra_sdk-2.1.7/doc/help/html/fastq-load-help.html0000644001221300116200000000353511627507276021166 0ustar rodarmertrace fastq-load help 
Usage:
  fastq-load [options] -r run.xml -e experiment.xml -o output-path

  -r|--run-xml                     path to run.xml describing input files
  -e|--experiment                  path to experiment.xml
  -o|--output-path                 target location

Options:
  -i|--input-path                  input files location, default '.'
  -u|--input-unpacked              input files are unpacked
  -f|--force                       force target overwrite
  -n|--spots-number                process only given number of spots from input
  -b|--bad-spot-number             acceptable number of spot creation errors, default is 50
  -p|--bad-spot-percentage         acceptable percentage of spots creation errors, default is 5
  -x|--expected                    path to expected.xml
  -z|--xml-log                     produce XML-formatted log file
  -s|--intensities                 [on | off] load intensity data, default is off:
                                     Illumina: signal, intensity, noise;
                                     AB SOLiD: signal(s);
                                     LS454: signal, position (for SFF files ON by default).

  -h|--help                        Output a brief explantion for the program.
  -V|--version                     Display the version of the program then quit.
  -L|--log-level <level>           Logging level as number or enum string.
                                   One of (fatal|sys|int|err|warn|info) or (0-5)
                                   Current/default is warn
  -v|--verbose                     Increase the verbosity level of the program.
                                   Use multiple times for more verbosity.
sra_sdk-2.1.7/doc/help/html/illumina-dump-help.html0000644001221300116200000000443411627507276021707 0ustar rodarmertrace illumina-dump help 
Usage:
  illumina-dump [options] [ -A ] <accession>
  illumina-dump [options] <path>

  -A|--accession <accession>       Replaces accession derived from <path> in filename(s) and deflines

Options:

  -O|--outdir <path>               Output directory, default is '.'
  -N|--minSpotId <rowid>           Minimum spot id
  -X|--maxSpotId <rowid>           Maximum spot id
  -G|--spot-group                  Split into files by SPOT_GROUP (member name)
  --spot-groups <[list]>           Filter by SPOT_GROUP (member): name[,...]
  -R|--read-filter <[filter]>      Split into files by READ_FILTER value
                                   optionally filter by a value: pass|reject|criteria|redacted
  -T|--group-in-dirs               Split into subdirectories instead of files
  -K|--keep-empty-files            Do not delete empty files
  --table <table-name>             (New) Table name within SRA format, default is SEQUENCE

  -h|--help                        Output a brief explantion for the program
  -V|--version                     Display the version of the program then quit
  -L|--log-level <level>           Logging level as number or enum string
                                   One of (fatal|sys|int|err|warn|info) or (0-5)
                                   Current/default is warn
  -v|--verbose                     Increase the verbosity level of the program
                                   Use multiple times for more verbosity

Format options:

  -r|--read                        Output READ: "seq", default is on
  -q|--qual1 <1|2>                 Output QUALITY, whole spot (1) or split by reads (2): "qcal", default is 1
  -p|--qual4                       Output full QUALITY: "prb", default is off
  -i|--intensity                   Output INTENSITY, if present: "int", default is off
  -n|--noise                       Output NOISE, if present: "nse", default is off
  -s|--signal                      Output SIGNAL, if present: "sig2", default is off
  -x|--qseq <1|2>                  Output QSEQ format: whole spot (1) or split by reads: "qseq", default is off
sra_sdk-2.1.7/doc/help/html/illumina-load-help.html0000644001221300116200000000354311627507276021661 0ustar rodarmertrace illumina-load help 
Usage:
  illumina-load [options] -r run.xml -e experiment.xml -o output-path

  -r|--run-xml                     path to run.xml describing input files
  -e|--experiment                  path to experiment.xml
  -o|--output-path                 target location

Options:
  -i|--input-path                  input files location, default '.'
  -u|--input-unpacked              input files are unpacked
  -f|--force                       force target overwrite
  -n|--spots-number                process only given number of spots from input
  -b|--bad-spot-number             acceptable number of spot creation errors, default is 50
  -p|--bad-spot-percentage         acceptable percentage of spots creation errors, default is 5
  -x|--expected                    path to expected.xml
  -z|--xml-log                     produce XML-formatted log file
  -s|--intensities                 [on | off] load intensity data, default is off:
                                     Illumina: signal, intensity, noise;
                                     AB SOLiD: signal(s);
                                     LS454: signal, position (for SFF files ON by default).

  -h|--help                        Output a brief explantion for the program.
  -V|--version                     Display the version of the program then quit.
  -L|--log-level <level>           Logging level as number or enum string.
                                   One of (fatal|sys|int|err|warn|info) or (0-5)
                                   Current/default is warn
  -v|--verbose                     Increase the verbosity level of the program.
                                   Use multiple times for more verbosity.
sra_sdk-2.1.7/doc/help/html/kar-help.html0000644001221300116200000000552111627507276017705 0ustar rodarmertrace kar help 
Usage:
  kar [OPTIONS] -c|--create <Archive> -d|--directory <Directory> [Filter ...]
  kar [OPTIONS] -x|--extract <Archive> -d|--directory <Directory>
  kar [OPTIONS] -t|--test|--list <Archive>

Summary:
  Create, extract from, or test an archive.

Archive Command:
  All of these options require the next token on the command line to be
  the name of the archive
  -c|--create <archive>            Create a new archive.
  -x|--extract <archive>           Extract the contents of an archive into a directory.
  -t|--test <archive>              Check the structural validity of an archive
                                   Optionally listing its contents

Archive:
  Path to a file that will/does hold the archive of other files

Directory:
    Required for create or extract command, ignored for test command

Filters:
  When present these act as include filters.
  Any file name will be included in the extracted files, created archive
  or test operation listing
  Any directory will be included as well as its contents

Options:
  -d|--directory <Directory>       The next token on the command line is the
                                   name of the directory to extract to or create
                                   from
  -f|--force                       (no parameter) this will cause the extract or
                                   create to over-write existing files unless
                                   they are write-protected.  without this
                                   option the program will fail if the archive
                                   already exists for a create or the target
                                   directory exists for an extract
  -a|--align <alignment>           Forces the alignment of files in create
                                   mode putting the first byte of included
                                   files at <alignment boundaries
                                   alignment: 1|2|4|8
                                   (default=4)
  -l|--long-list                   more information will be given on each file
                                   in test/list mode.

  -h|--help                        Output a brief explantion for the program.
  -V|--version                     Display the version of the program then quit.
  -L|--log-level <level>           Logging level as number or enum string.
                                   One of (fatal|sys|int|err|warn|info) or (0-5)
                                   Current/default is warn
  -v|--verbose                     Increase the verbosity level of the program.
                                   Use multiple times for more verbosity.
sra_sdk-2.1.7/doc/help/html/kdbmeta-help.html0000644001221300116200000000372011627507276020536 0ustar rodarmertrace kdbmeta help 
Usage:
  kdbmeta [Options] <target> {<query> ...]

Summary:
  Display the contents of one or more metadata stores.
  The target metadata are described by one or more
  target specifications, giving the path to a database, a table
  or a column. the command and query are executed on each target.

  queries name one or more objects, and '*' acts as a wildcard.
  query objects are nodes or attributes. nodes are named with a
  hierarchical path, like a file-system path. attributes are given
  as a node path followed by a '@' followed by the attribute name.

target:
  path-to-database                 access database metadata
  path-to-table                    access table metadata
  path-to-column                   access column metadata
  accession                        sra global access id

query:
  *                                all nodes and attributes
  NAME                             a named root node and children
  PATH/NAME                        an internal node and children
  <node>@ATTR                      a named attribute
  <obj>=VALUE                      a simple value assignment where
                                   value string is text, and binary
                                   values use hex escape codes

Options:
  -h|--help                        Output a brief explantion for the program.
  -V|--version                     Display the version of the program then quit.
  -L|--log-level <level>           Logging level as number or enum string.
                                   One of (fatal|sys|int|err|warn|info) or (0-5)
                                   Current/default is warn
  -v|--verbose                     Increase the verbosity level of the program.
                                   Use multiple times for more verbosity.
sra_sdk-2.1.7/doc/help/html/kqsh-help.html0000644001221300116200000000061011476747102020064 0ustar rodarmertrace kqsh help 
Usage: kqsh [ options ] [ file... ]

    options:
      -h               give tool help
      -u               enable update operations
      -l         path(s) for loading dynamic libraries
sra_sdk-2.1.7/doc/help/html/md5cp-help.html0000644001221300116200000000111711476747102020131 0ustar rodarmertrace md5cp help 
usage: md5cp [-p] [-f] [-r] [file|directory ...] directory

    md5cp [-f] source_filename dest_filename
    : Copies files and/or directories, creating an md5sum checksum (named file.md5) for all copied files.
    
-f forces replacement of existing files.
-p forces replacement of existing modes on files and directories.
-r recurses over source directories (directories are ignored otherwise)
sra_sdk-2.1.7/doc/help/html/rcexplain-help.html0000644001221300116200000000153211627507276021113 0ustar rodarmertrace rcexplain help 
Usage:
  rcexplain [Options] rc [rc ...]

Summary:
  Prints out error string to stdout for one or more return codes.

Options:
  -h|--help                        Output a brief explantion for the program.
  -V|--version                     Display the version of the program then quit.
  -L|--log-level <level>           Logging level as number or enum string.
                                   One of (fatal|sys|int|err|warn|info) or (0-5)
                                   Current/default is warn
  -v|--verbose                     Increase the verbosity level of the program.
                                   Use multiple times for more verbosity.
sra_sdk-2.1.7/doc/help/html/sff-dump-help.html0000644001221300116200000000320511627507276020646 0ustar rodarmertrace sff-dump help 
Usage:
  sff-dump [options] [ -A ] <accession>
  sff-dump [options] <path>

  -A|--accession <accession>       Replaces accession derived from <path> in filename(s) and deflines

Options:

  -O|--outdir <path>               Output directory, default is '.'
  -N|--minSpotId <rowid>           Minimum spot id
  -X|--maxSpotId <rowid>           Maximum spot id
  -G|--spot-group                  Split into files by SPOT_GROUP (member name)
  --spot-groups <[list]>           Filter by SPOT_GROUP (member): name[,...]
  -R|--read-filter <[filter]>      Split into files by READ_FILTER value
                                   optionally filter by a value: pass|reject|criteria|redacted
  -T|--group-in-dirs               Split into subdirectories instead of files
  -K|--keep-empty-files            Do not delete empty files
  --table <table-name>             (New) Table name within SRA format, default is SEQUENCE

  -h|--help                        Output a brief explantion for the program
  -V|--version                     Display the version of the program then quit
  -L|--log-level <level>           Logging level as number or enum string
                                   One of (fatal|sys|int|err|warn|info) or (0-5)
                                   Current/default is warn
  -v|--verbose                     Increase the verbosity level of the program
                                   Use multiple times for more verbosity
sra_sdk-2.1.7/doc/help/html/sra-dump-help.html0000644001221300116200000000223711627507276020661 0ustar rodarmertrace sra-dump help 
Usage:
  sra-dump [ options ] table [ column-spec ... ]

Summary:
  Dump all data in table for specified or all columns

table:
  path to table or accession id within NCBI

column-spec:
  NAME                             simple column name
  (typedecl)NAME                   specifically typed column name

Options:
  --start <ID>                     beginning spot id (default 1)
  --stop <ID>                      ending spot id (default max)

  -h|--help                        Output a brief explantion for the program.
  -V|--version                     Display the version of the program then quit.

  -L|--log-level <level>           Logging level as number or enum string.
                                   One of (fatal|sys|int|err|warn|info) or (0-5)

                                   Current/default is warn
  -v|--verbose                     Increase the verbosity level of the program.
                                   Use multiple times for more verbosity.
sra_sdk-2.1.7/doc/help/html/sra-stat-help.html0000644001221300116200000000226511627507276020670 0ustar rodarmertrace sra-stat help 
Usage:
  sra-stat [options] table

Summary:
  Display table statistics

Options:
  -x|--xml                         output as XML (default is text)
  -b|--start <row-id>              starting spot id ( default 1 )
  -e|--stop <row-id>               ending spot id ( default max )
  -m|--meta                        print load metadata
  -q|--quick                       quick mode: get statistics from metadata
                                   not to scan the table

  -h|--help                        Output a brief explantion for the program.
  -V|--version                     Display the version of the program then quit.
  -L|--log-level <level>           Logging level as number or enum string.
                                   One of (fatal|sys|int|err|warn|info) or (0-5)
                                   Current/default is warn
  -v|--verbose                     Increase the verbosity level of the program.
                                   Use multiple times for more verbosity.
sra_sdk-2.1.7/doc/help/html/srapath-help.html0000644001221300116200000000334011476747102020563 0ustar rodarmertrace srapath help 
Usage:
 srapath 1.2.0

Usage: srapath [ options ] accession ...

    options:
      --server        path(s) to replication server(s)
      --volume           relative path(s) to volume(s)

    Tool to produce a list of full paths to SRA runs from list of
    accessions.  Output paths are ordered according to accession list.
    with no path alteration options, the accession search path will be
    determined according to the local installation.
    Replication server and volume paths may be compound, adhering to the
    Unix path convention of ':' separators, e.g.

        '/server1:/server2/subdir'

    The idea behind separate replication servers and volumes is to
    allow for a matrix of volumes that can hold a run, where the volumes
    are expected to be replicated across all repservers.  It is possible that
    this arrangement will be violated and still work, but behavior is less
    clearly defined.

    The order of search paths is important: rather than alphabetical,
    specify paths in the preferred order of discovery, usually giving the most
    recently updated volumes first.  If a run appears more than once in the matrix,
    it will be found according to the first 'repserver/volume' combination that
    produces a hit.

    Finally, this tool produces a path that is 'likely' to be a run, in that
    an entry exists in the file system at the location predicted.  It is possible
    that this path will fail to produce success upon opening a run if the path does
    not point to a valid object.
sra_sdk-2.1.7/doc/help/html/srf-load-help.html0000644001221300116200000000353011627507276020635 0ustar rodarmertrace srf-load help 
Usage:
	srf-load [options] -r run.xml -e experiment.xml -o output-path

  -r|--run-xml                     path to run.xml describing input files
  -e|--experiment                  path to experiment.xml
  -o|--output-path                 target location

Options:
  -i|--input-path                  input files location, default '.'
  -u|--input-unpacked              input files are unpacked
  -f|--force                       force target overwrite
  -n|--spots-number                process only given number of spots from input
  -b|--bad-spot-number             acceptable number of spot creation errors, default is 50
  -p|--bad-spot-percentage         acceptable percentage of spots creation errors, default is 5
  -x|--expected                    path to expected.xml
  -z|--xml-log                     produce XML-formatted log file
  -s|--intensities                 [on | off] load intensity data, default is off:
                                     Illumina: signal, intensity, noise;
                                     AB SOLiD: signal(s);
                                     LS454: signal, position (for SFF files ON by default).

  -h|--help                        Output a brief explantion for the program.
  -V|--version                     Display the version of the program then quit.
  -L|--log-level <level>           Logging level as number or enum string.
                                   One of (fatal|sys|int|err|warn|info) or (0-5)
                                   Current/default is warn
  -v|--verbose                     Increase the verbosity level of the program.
                                   Use multiple times for more verbosity.
sra_sdk-2.1.7/doc/help/html/txt2kdb-help.html0000644001221300116200000000413711476747102020510 0ustar rodarmertrace txt2kdb help 
 txt2kdb [Options] FILE KCOLUMN
    Create a KColumn physical column out of a text file.

    FILE:
        The text file should be ASCII or UTF-8 using LF, CR or CR-LF
        line termination.  Each text line will be put into the
        KColumn as a separate Row.  Each Row will be in its own
        blob.
    KCOLUMN:
        The KColumn is either an existing KColumn or a path to one
        that can be created.    Both paths should be relative to the current directory or full
    from root "/"

Options:
  -b, --begin=START         include only lines starting from this line in the
                            KColumn.  The first line is line 1 (not 0).
  -e, --end=STOP            stop including lines after this line in the
                            KColumn.  The first line is line 1 (not 0).
  -f, --force               (no parameter) this will cause to over-write
                            existing files.  Without
                            this option the program will fail if the KColumn
                            already exists and append mode is not selected
  -a, --append              (no parameter) this will cause to append the text
                            file to an existing KColumn.  If the file does not
                            already exist it will be created.
  -V, --version             this will cause the program to emit the internal
                            version number before any other action
  -v, --verbose             extra information will be output during
                            processing second occurrence on the command line
                            means even more
  -h, -?, --help            print this message
  -l, --log-level=LEVEL     the next token will affect the logging level of
                            the program  accepted tokens are the numbers
                            0-15, fatal, sys, int, err, warn, info
                          , debug1...debug10
sra_sdk-2.1.7/doc/help/html/vdb-dump-help.html0000644001221300116200000000374411645077605020651 0ustar rodarmertrace vdb-dump help 
Usage:
  vdb-dump <path> [options]

Options:
  -I|--row_id_on                   print row id
  -l|--line_feed <line_feed>       line-feed's inbetween rows
  -N|--colname_off                 do not print column-names
  -X|--in_hex                      print numbers in hex
  -T|--table <table>               table-name
  -R|--rows <rows>                 rows (default = all)
  -C|--columns <columns>           columns (default = all)
  -S|--schema <schema>             schema-name
  -A|--schema_dump                 dumps the schema
  -E|--table_enum                  enumerates tables
  -O|--column_enum                 enumerates columns in extended form
  -o|--column_enum_short           enumerates columns in short form 
  -D|--dna_bases <dna_bases>       print dna-bases
  -M|--max_length <max_length>     limits line length
  -i|--indent_width <indent_width> indents the line
  -f|--format <format>             dump format (csv,xml,json,piped,tab)
  -r|--id_range                    prints id-range
  -n|--without_sra                 without sra-type-translation
  -a|--without_accession           without accession-test
  -x|--exclude                     exclude these columns
  -b|--boolean                     defines how boolean's are printed (1,T) 

  -h|--help                        Output a brief explantion for the program.
  -V|--version                     Display the version of the program then quit.
  -L|--log-level <level>           Logging level as number or enum string.
                                   One of (fatal|sys|int|err|warn|info) or (0-5)
                                   Current/default is warn
  -v|--verbose                     Increase the verbosity level of the program.
                                   Use multiple times for more verbosity.
sra_sdk-2.1.7/doc/help/txt/0000755001221300116200000000000011477730356015164 5ustar rodarmertracesra_sdk-2.1.7/doc/help/txt/abi-dump-help.txt0000644001221300116200000000151411476747102020346 0ustar rodarmertraceUsage: abi-dump -path [-outdir ] [-minSpotId ] [-maxSpotId ] [-minReadLen ] [-noclip] [-origfmt] [-noDotReads] Where: -accession Run accession - top level directory for SRA format either downloaded or locally generated -path Path to (but not including) accession -outdir Output directory (defaults to current directory) -minSpotId Minimum spot id to output -maxSpotId Maximum spot id to output -minReadLen Minimum read length to output (defaults is 25) -noclip Indicates don't apply clip quality right -origfmt Excludes SRR accession & length on defline -noDotReads No reads consisting only of dots are output -noSignal Do not write sginal files sra_sdk-2.1.7/doc/help/txt/abi-load-help.txt0000644001221300116200000000310411476747102020315 0ustar rodarmertraceUsage: abi-load abi-load [ ] [ ] input-spec: ( -r | --run-xml ) path # path to run.xml describing input files spot-descriptor: ( -e | --experiment ) path # path to experiment.xml # with spot descriptor output-spec: # produce output to run output-mode: -c | --create # create only new run (fail if exists) -o | --output # create new or replace existing run -a | --append # create new or update existing run run-name: path # full or working-directory relative # file-system path to run options: ( -n | --spotnumber) spots_to_run # tells the loader to stop processing after that many spots # helpful in testing ( -b | --bad-spot-number ) bad_spot_number # number of spot creation errors to be tolerated # default = 50 ( -p | --bad-spot-percentage ) bad_spot_percentage> # PERCENTAGE of the number of bad spots against # the number of good spots, default = 5 help: ( -h | --help ) # print usage and option details verbosity: ( -l | --log-level ) #logging level: fatal|sys|int|err|warn|info default=info debug: ( -+ | --debug ) #module: APP|KFS|XML|VDB|SRA|REF|LEGREF default=APP sra_sdk-2.1.7/doc/help/txt/bam-loader-help.txt0000644001221300116200000000145111476747102020653 0ustar rodarmertraceUsage: bam-loader 0.0.1 bam-loader [Options] BAMFILE Load a bam file. Options: -o, --output=TABLEPATH REQUIRED: path to a table where the table will be put -V, --version this will cause the program to emit the internal version number before any other action -v, --verbose extra information will be output during processing second occurrence on the command line means even more -h, -?, --help print this message -l, --log-level=LEVEL the next token will affect the logging level of the program accepted tokens are the numbers 0-15, fatal, sys, int, err, warn, info , debug1...debug10 sra_sdk-2.1.7/doc/help/txt/copycat-help.txt0000644001221300116200000000441711476747102020317 0ustar rodarmertrace copycat : 1.0.6 Usage: copycat [ ] src-file dst-file copycat [ ] src-file [src-file...] dst-dir copycat [ ] -o dst-dir src-file [src-file...] options: -x cache-dir location to output cached files -f force overwrite of existing files -m magicfile path to the magic file to use -e extfile path to the extensions file to use -c classfile path to the file class/type file behavior is intended to mimic 'cp' to a large extent, in that a single source file may be copied to a new name, or multiple source files may be copied to a destination directory. when the destination directory is specified using 'cp' semantics, the directory must exist. if specified via '-o' switch, it will be created if necessary. the target file may also be a device. in the special case of /dev/null, it may also act as a directory. the '-x' option allows small files that are typed as eligible for caching to be copied to the cache directory provided. the directory will be created if necessary. the intent is to capture top-level files, such that files are copied into the flat cache directory without regard to where they were found in the input hierarchy. in the case of name conflict, output files will be renamed. the class file, magic file and extension file allow new understandings of files found while cataloging the magic file is of the type used by the unix/linux 'file' command the class file assigns file type to classes the extension file assigns file extensions to file types existing classes are 'Archive', 'Cached', 'Compressed', 'Read' Archive and Compresses files are those that have contents that can be examined - new types must be compiled in Cached files are those affected by the -x option Read files are not handled seperately by copy cat except in the catalog new classes would like Read only be added to the catalog with the class the format for the class file is lines such as the below 'GnuZipCompressed' with tabs and linefeeds the format for the extension file is lines such as the below 'gzCompressed' with tabs and linefeeds sra_sdk-2.1.7/doc/help/txt/crc32sum-help.txt0000644001221300116200000000022711476747102020311 0ustar rodarmertrace: usage: crc32sum [