debian/0000755000000000000000000000000012240000730007152 5ustar debian/bin/0000755000000000000000000000000011736313146007743 5ustar debian/bin/snap0000644000000000000000000000007011736313146010624 0ustar #!/bin/sh ZOE=/usr/share/snap/Zoe /usr/lib/snap/snap $@ debian/watch0000644000000000000000000000010211576504570010222 0ustar version=3 http://homepage.mac.com/iankorf/snap-([0-9-]+)\.tar\.gz debian/snap.dirs0000644000000000000000000000003311576505753011024 0ustar usr/bin usr/share/snap/Zoe debian/copyright0000644000000000000000000000225211736102663011127 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: SNAP Upstream-Contact: ik1@sanger.ac.uk Source: http://homepage.mac.com/iankorf/snap-2010-07-28.tar.gz Files: * Copyright: 2002-2005 Ian Korf UC Davis Genome Center, Davis, CA, USA License: GPL-2.0+ Files: debian/* Copyright: 2011 Steffen Moeller License: GPL-2.0+ License: GPL-2.0+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". debian/snap.install0000644000000000000000000000072312237747404011533 0ustar exonpairs usr/bin hmm-info usr/bin forge usr/bin fathom usr/bin snap usr/lib/snap debian/bin/snap usr/bin cds-trainer.pl usr/bin hmm-assembler.pl usr/bin noncoding-trainer.pl usr/bin patch-hmm.pl usr/bin zff2gff3.pl usr/bin HMM usr/share/snap Zoe/zoe-loop usr/bin Zoe/blosum62 usr/share/snap/Zoe # dh_installmans is to intelligent and moves these manpages to /usr/share/man/pl/man1 which is prevented by this trick debian/mans.pl/* usr/share/man/man1 debian/manpages0000644000000000000000000000002012237207601010674 0ustar debian/mans/*.1 debian/changelog0000644000000000000000000000256712240000641011037 0ustar snap (2010-07-28-2) unstable; urgency=low * debian/upstream: Added citation information * debian/copyright: DEP5 issues * debian/README.Debian: - Removed information which is not intended for users - Added information about scripts which are not included into the package since some requriements are not yet fullfilled * debian/control: - cme fix dpkg-control - canonical Vcs fields * debhelper 9 (control+compat) * debian/patches/unused-but-set-variable.patch: Make sure package builds with hardening flags * debian/rules: - deleted useless comment - Work around self-made build system and save original files before configuration and restore these in clean target * debian/mans: create simple man pages by polishing help2man output * debian/bin/snap: wrapper to set environment variable ZOE to implement hint given in 00README installation instructions * debian/patches/hardening.patch: Propagate hardening options -- Andreas Tille Fri, 25 Oct 2013 16:39:26 +0200 snap (2010-07-28-1~lucid1) lucid; urgency=low * Building for Debian PPA -- Steffen Moeller Fri, 17 Jun 2011 00:52:13 +0200 snap (2010-07-28-1) experimental; urgency=low * Crude initial release, lacking man pages (Closes: #630753). -- Steffen Moeller Fri, 17 Jun 2011 00:52:12 +0200 debian/mans.pl/0000755000000000000000000000000012237750003010535 5ustar debian/mans.pl/hmm-assembler.pl.10000644000000000000000000000324412237211532013767 0ustar .TH HMM-ASSEMBLER.PL "1" "November 2013" "hmm-assembler.pl 2010-07-28" "User Commands" .SH NAME hmm-assembler.pl \- SNAP module hmm-assembler.pl .SH SYNOPSIS .B hmm-assembler.pl [\fI-OPTIONS \fR[\fI-MORE_OPTIONS\fR]] [\fI--\fR] [\fIPROGRAM_ARG1 \fR...] .SH OPTIONS .SS "The following single-character options are accepted:" .PP With arguments: \fB\-i\fR \fB\-e\fR \fB\-A\fR \fB\-D\fR \fB\-M\fR \fB\-S\fR \fB\-C\fR \fB\-I\fR \fB\-N\fR \fB\-a\fR \fB\-3\fR \fB\-5\fR \fB\-Z\fR \fB\-c\fR .PP Boolean (without arguments): \fB\-r\fR \fB\-o\fR \fB\-x\fR \fB\-p\fR \fB\-t\fR \fB\-1\fR .PP Options may be merged together. \fB\-\-\fR stops processing of options. Space is not required between options and their arguments. .PP Options: .TP \fB\-i\fR [500] .TP \fB\-e\fR [1000] .TP \fB\-A\fR [0:30] .TP \fB\-D\fR [0:9] .TP \fB\-M\fR [0:15] .TP \fB\-S\fR [0:9] .TP \fB\-C\fR [4] .TP \fB\-I\fR [4] .TP \fB\-N\fR [4] .TP \fB\-3\fR [] include 3'UTR model, requires \fB\-a\fR .TP \fB\-a\fR [] include PolyA model, requires \fB\-3\fR .TP \fB\-5\fR [] include 5'UTR moel, requires \fB\-p\fR .TP \fB\-p\fR include generic promoter model, requires \fB\-5\fR .TP \fB\-r\fR include generic repeat model .TP \fB\-o\fR include reverse ORF model .TP \fB\-x\fR use explicit duration intron model .TP \fB\-t\fR include C.elegans trans\-splicing, requires \fB\-p\fR, \fB\-5\fR .TP \fB\-Z\fR sets clade\-specific values (worm, fly, plant) .TP \fB\-1\fR single gene model .TP \fB\-c\fR include GC\-AG splice donor model debian/mans.pl/patch-hmm.pl.10000644000000000000000000000037512237750003013114 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3. .TH PATCH-HMM.PL "1" "October 2013" "patch-hmm.pl 2010-07-28" "User Commands" .SH NAME patch-hmm.pl \- SNAP module patch-hmm.pl .SH SYNOPSIS .B patch\-hmm.pl debian/mans.pl/zff2gff3.pl.10000644000000000000000000000033412237747775012674 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3. .TH ZFF2GFF3.PL "1" "October 2013" "SNAP 2010-07-28" "User Commands" .SH NAME zff2gff3.pl \- SNAP module zff2gff3.pl .SH SYNOPSIS .B zff2gff3.pl debian/README.Debian0000644000000000000000000000114112240000477011220 0ustar snap for Debian --------------- The Perl scripts cds-trainer.pl and noncoding-trainer.pl are needing the following Perl modules: IK.pm, FAlite.pm, DataBrowser.pm A web search leads to https://github.com/KorfLab/LearnGit which is a bit mysterious because it is a "Git learning" project and no serious bio informatics Perl module. Since this all seems a bit strange it was decided to drop the two Perl scripts with unavailable Perl modules and the user who might really need these is asked to provide more detailed information. -- Andreas Tille Fri, 25 Oct 2013 16:39:26 +0200 debian/source/0000755000000000000000000000000011576511543010476 5ustar debian/source/format0000644000000000000000000000001411576504437011710 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000211736103232010362 0ustar 9 debian/patches/0000755000000000000000000000000012232504235010613 5ustar debian/patches/series0000644000000000000000000000005612232502367012035 0ustar unused-but-set-variable.patch hardening.patch debian/patches/hardening.patch0000644000000000000000000000673412232504235013605 0ustar Author: Andreas Tille LastChanged: Fri, 25 Oct 2013 16:39:26 +0200 Description: Propagate Hardening options --- a/Makefile +++ b/Makefile @@ -2,6 +2,8 @@ # Makefile for SNAP # ###################### +export CFLAGS LDFLAGS + LIB = -lm INC = -IZoe @@ -58,19 +60,19 @@ default: make gcc $(APP): $(OBJ) $(OBJECTS) - $(CC) -o $(APP) $(CFLAGS) $(OBJ) $(OBJECTS) $(LIB) + $(CC) -o $(APP) $(CFLAGS) $(OBJ) $(OBJECTS) $(LIB) $(LDFLAGS) $(APP2): $(OBJ2) $(OBJECTS) - $(CC) -o $(APP2) $(CFLAGS) $(OBJ2) $(OBJECTS) $(LIB) + $(CC) -o $(APP2) $(CFLAGS) $(OBJ2) $(OBJECTS) $(LIB) $(LDFLAGS) $(APP3): $(OBJ3) $(OBJECTS) - $(CC) -o $(APP3) $(CFLAGS) $(OBJ3) $(OBJECTS) $(LIB) + $(CC) -o $(APP3) $(CFLAGS) $(OBJ3) $(OBJECTS) $(LIB) $(LDFLAGS) $(APP4): $(OBJ4) $(OBJECTS) - $(CC) -o $(APP4) $(CFLAGS) $(OBJ4) $(OBJECTS) $(LIB) + $(CC) -o $(APP4) $(CFLAGS) $(OBJ4) $(OBJECTS) $(LIB) $(LDFLAGS) $(APP5): $(OBJ5) $(OBJECTS) - $(CC) -o $(APP5) $(CFLAGS) $(OBJ5) $(OBJECTS) $(LIB) + $(CC) -o $(APP5) $(CFLAGS) $(OBJ5) $(OBJECTS) $(LIB) $(LDFLAGS) clean: rm -f *.o $(APP) $(APP2) $(APP3) $(APP4) $(APP5) @@ -93,12 +95,12 @@ tar: ################# gcc: - cd Zoe; make; - make $(APP) CC="gcc" CFLAGS="-O2 -Wall -Werror" - make $(APP2) CC="gcc" CFLAGS="-O2 -Wall -Werror" - make $(APP3) CC="gcc" CFLAGS="-O2 -Wall -Werror" - make $(APP4) CC="gcc" CFLAGS="-O2 -Wall -Werror" - make $(APP5) CC="gcc" CFLAGS="-O2 -Wall -Werror" + cd Zoe; make CFLAGS="$(CFLAGS)"; + make $(APP) CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)" + make $(APP2) CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)" + make $(APP3) CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)" + make $(APP4) CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)" + make $(APP5) CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)" ################### --- a/Zoe/Makefile +++ b/Zoe/Makefile @@ -55,22 +55,22 @@ DATE = $(shell date +\%Y-\%m-\%d) ########### default: - make gcc + make gcc CFLAGS="$(CFLAGS)" $(APP): $(OBJ) $(OBJECTS) - $(CC) -o $(APP) $(CFLAGS) $(OBJ) $(OBJECTS) $(LIB) + $(CC) -o $(APP) $(CFLAGS) $(OBJ) $(OBJECTS) $(LIB) $(LDFLAGS) $(APP2): $(OBJ2) $(OBJECTS) - $(CC) -o $(APP2) $(CFLAGS) $(OBJ2) $(OBJECTS) $(LIB) + $(CC) -o $(APP2) $(CFLAGS) $(OBJ2) $(OBJECTS) $(LIB) $(LDFLAGS) $(APP3): $(OBJ3) $(OBJECTS) - $(CC) -o $(APP3) $(CFLAGS) $(OBJ3) $(OBJECTS) $(LIB) + $(CC) -o $(APP3) $(CFLAGS) $(OBJ3) $(OBJECTS) $(LIB) $(LDFLAGS) $(APP4): $(OBJ4) $(OBJECTS) - $(CC) -o $(APP4) $(CFLAGS) $(OBJ4) $(OBJECTS) $(LIB) + $(CC) -o $(APP4) $(CFLAGS) $(OBJ4) $(OBJECTS) $(LIB) $(LDFLAGS) $(APP5): $(OBJ5) $(OBJECTS) - $(CC) -o $(APP5) $(CFLAGS) $(OBJ5) $(OBJECTS) $(LIB) + $(CC) -o $(APP5) $(CFLAGS) $(OBJ5) $(OBJECTS) $(LIB) $(LDFLAGS) clean: rm -f *.o $(APP) $(APP2) $(APP3) $(APP4) $(APP5) @@ -92,14 +92,14 @@ tar: ################# gcc: - make $(APP) CC="gcc" CFLAGS="-O2 -Wall -Werror" + make $(APP) CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)" all: - make $(APP) CC="gcc" CFLAGS="-O2 -Wall -Werror" - make $(APP2) CC="gcc" CFLAGS="-O2 -Wall -Werror" - make $(APP3) CC="gcc" CFLAGS="-O2 -Wall -Werror" - make $(APP4) CC="gcc" CFLAGS="-O2 -Wall -Werror" - make $(APP5) CC="gcc" CFLAGS="-O2 -Wall -Werror" + make $(APP) CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)" + make $(APP2) CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)" + make $(APP3) CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)" + make $(APP4) CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)" + make $(APP5) CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)" ################### debian/patches/unused-but-set-variable.patch0000644000000000000000000000567311736122244016322 0ustar Author: Andreas Tille Date: Sun, 01 Apr 2012 18:40:17 +0200 Description: When enabling hardening flags by using debhelper 9 unsused variables should not be assigned. This patch comments those variables. --- snap-2010-07-28.orig/Zoe/zoeAlignment.c +++ snap-2010-07-28/Zoe/zoeAlignment.c @@ -720,15 +720,15 @@ zoeVec zoeChainHSPs (const zoeVec HSPs) { int i; zoeVec bestHSPs = NULL; /* shush */ - zoeVec qvec; - zoeVec svec; + /* zoeVec qvec; */ + /* zoeVec svec; */ for (i = 0; i < HSPs->size; i++) { zoeWriteHSP(stdout, HSPs->elem[i]); } - qvec = zoeGroupHSPs(HSPs, 'q'); - svec = zoeGroupHSPs(HSPs, 's'); + /* qvec = */ zoeGroupHSPs(HSPs, 'q'); + /* svec = */ zoeGroupHSPs(HSPs, 's'); return bestHSPs; } --- snap-2010-07-28.orig/Zoe/zoeCDS.c +++ snap-2010-07-28/Zoe/zoeCDS.c @@ -396,7 +396,7 @@ char text[256]; struct exon_feature efstart, efstop; struct best_translation bt; - int i, nt_length, elength, inc5, inc3, frame, idx, b1, b2, b3, b4, all_exon, split; + int i, nt_length, elength, inc5, inc3, frame, idx, b1, b2, b3, b4, /* all_exon, */ split; int exstart, exend, exinc; /* assigned immediately */ @@ -483,10 +483,10 @@ } /* re-label generic exons as Einit, Eterm, Esngl only if all exons defined as Exon */ - all_exon = 1; + /* all_exon = 1; */ for (i = 0; i < cds->exons->size; i++) { if (cds->exons->elem[i]->label != Exon) { - all_exon = 0; + /* all_exon = 0; */ break; } } --- snap-2010-07-28.orig/Zoe/zoeFeature.c +++ snap-2010-07-28/Zoe/zoeFeature.c @@ -167,7 +167,7 @@ zoeFeature zoeReadGFF (FILE * stream) { char line[1024], Source[64], ID[64], Label[64], Start[16], End[16], Strand[8], Score[32], Frame[8], Group[512]; - char * group = NULL; + /* char * group = NULL; */ zoeLabel label; coor_t start, end; strand_t strand; @@ -178,10 +178,10 @@ if (sscanf(line, "%s %s %s %s %s %s %s %s %s", /* group */ Source, ID, Label, Start, End, Score, Strand, Frame, Group) == 9) { - group = Group; + /* group = Group */ ; } else if (sscanf(line, "%s %s %s %s %s %s %s %s", /* no group */ Source, ID, Label, Start, End, Score, Strand, Frame) == 8) { - group = NULL; + /* group = NULL */ ; } else { zoeWarn("zoeReadGFF format not valid"); return NULL; --- snap-2010-07-28.orig/Zoe/zoeFeatureFactory.c +++ snap-2010-07-28/Zoe/zoeFeatureFactory.c @@ -280,7 +280,7 @@ int f0, f1, f2; int * fstop; coor_t i; - int frame; /* should be frame_t, but screw casting */ + /* int frame; *//* should be frame_t, but screw casting */ zoeDNA dna = cds_scan->dna; zoeFeatureFactory factory = zoeMalloc(sizeof(struct zoeFeatureFactory)); @@ -334,7 +334,7 @@ fstop[2] = 2; for (i = 3; i < dna->length; i++) { - frame = i % 3; + /* frame = i % 3; */ if (stop[i] != MIN_SCORE) { fstop[i] = i; } else { debian/rules0000755000000000000000000000215012237747531010257 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') mandir=$(CURDIR)/debian/$(pkg)/usr/share/man/man1/ bindir=$(CURDIR)/debian/$(pkg)/usr/bin libdir=$(CURDIR)/debian/$(pkg)/usr/lib/snap version=$(shell dpkg-parsechangelog | grep '^Version:' | sed 's/^Version: \(.*\)-[^-]\+$$/\1/') %: dh $@ override_dh_auto_clean: touch depend Zoe/depend dh_auto_clean if [ -f depend.orig ] ; then mv depend.orig depend; fi if [ -f Zoe/depend.orig ] ; then mv Zoe/depend.orig Zoe/depend; fi override_dh_auto_config: cp -a depend depend.orig cp -a Zoe/depend Zoe/depend.orig dh_auto_config override_dh_auto_build: dh_auto_build CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" override_dh_install: dh_install # cds-trainer.pl and noncoding-trainer.pl are needing the following Perl modules: # IK.pm, FAlite.pm, DataBrowser.pm # since these are not available in Debian there is no point in installing this script find debian -name cds-trainer.pl -delete find debian -name noncoding-trainer.pl -delete debian/snap.examples0000644000000000000000000000000411576505601011667 0ustar DNA debian/control0000644000000000000000000000147412232501343010572 0ustar Source: snap Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Section: science Priority: extra Build-Depends: debhelper (>= 9), help2man Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/snap/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/snap/trunk/ Homepage: http://homepage.mac.com/iankorf/ Package: snap Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: location of genes from DNA sequence with hidden markov model SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser. debian/mans/0000755000000000000000000000000012237747643010143 5ustar debian/mans/fathom.10000644000000000000000000000157712237203137011476 0ustar .TH FATHOM "1" "October 2013" "fathom 2010-07-28" "User Commands" .SH NAME fathom \- sequence and annotation tool .SH SYNOPSIS .B fathom <\fBann\fR> <\fBdna\fR> <\fBcommands\fR> .SH OPTIONS .TP \fB\-help\fR report useful information .HP \fB\-validate\fR [\-quiet] .HP \fB\-gene\-stats\fR [\-errors\-ok \fB\-nucleotide\fR \fB\-dinucleotide]\fR .HP \fB\-categorize\fR .HP \fB\-export\fR [\-plus \fB\-errors\-ok]\fR .HP \fB\-extract\fR \fB\-length\fR \fB\-offset\fR .HP \fB\-exon\-intron\fR .HP \fB\-split\fR <\-number | \fB\-training\fR | \fB\-GC\fR | \fB\-repeat\fR > .HP \fB\-ace\-format\fR <\-gene\-method [\-dna \fB\-extra\fR ]> .HP \fB\-compare\-genes\fR [\-details] .HP \fB\-score\-genes\fR [\-errors\-ok] .HP \fB\-filter\-genes\fR \fB\-min\-score\fR \fB\-min\-length\fR debian/mans/snap.10000644000000000000000000000144012237207343011151 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3. .TH SNAP "1" "October 2013" "snap 2010-07-28" "User Commands" .SH NAME snap \- Semi-HMM-based Nucleic Acid Parser .SH SYNOPSIS .B snap [\fIoptions\fR] <\fBHMM file\fR> <\fBFASTA file\fR> [\fIoptions\fR] .SH OPTIONS .TP \fB\-help\fR report useful information .TP \fB\-lcmask\fR treat lowercase as N .TP \fB\-plus\fR predict on plus strand only .TP \fB\-minus\fR predict on minus strand only .TP \fB\-gff\fR output annotation as GFF .TP \fB\-ace\fR output annotation as ACED .TP \fB\-quiet\fR do not send progress to STDERR .TP \fB\-aa\fR create FASTA file of proteins .TP \fB\-tx\fR create FASTA file of transcripts .TP \fB\-xdef\fR external definitions .TP \fB\-name\fR name for the gene [default snap] debian/mans/exonpairs.10000644000000000000000000000173412237203131012215 0ustar .TH EXONPAIRS "1" "October 2013" "exonpairs 2010-07-28" "User Commands" .SH NAME exonpairs \- SNAP module exonpairs .SH SYNOPSIS .B exonpairs [\fIoptions\fR] <\fBHMM file\fR> <\fBFASTA file\fR> [\fIoptions\fR] .SH OPTIONS .TP \fB\-min\-intron\fR minimum Intron length [30] .TP \fB\-max\-intron\fR maximum Intron length [10000] .TP \fB\-einit\-length\fR minimum Einit length in bp [10] .TP \fB\-eterm\-length\fR minimum Eterm length in bp [10] .TP \fB\-exon\-length\fR minimum Exon length in bp [30] .HP \fB\-intron\-score\fR minimum Intron score in bits [\-5] .TP \fB\-einit\-score\fR minimum Einit score in bits [\-5] .TP \fB\-eterm\-score\fR minimum Eterm score in bits [\-5] .TP \fB\-exon\-score\fR minimum Exon score in bits [\-5] .TP \fB\-pair\-score\fR minimum pair score (exon\-intron\-exon) [10] .TP \fB\-flank\-length\fR length of flanking sequence per exon [20] .TP \fB\-lcmask\fR treat lowercase as N debian/mans/forge.10000644000000000000000000000135612237203740011315 0ustar .TH FORGE "1" "October 2013" "forge 2010-07-28" "User Commands" .SH NAME forge \- training program for SNAP .SH SYNOPSIS .B forge [\fIoptions\fR] <\fBann\fR> <\fBdna\fR> [\fIoptions\fR] .SH OPTIONS .HP \fB\-help\fR .HP \fB\-verbose\fR .TP \fB\-pseudocount\fR [1] (absolute number for all models) .HP \fB\-pseudoCoding\fR [0.0] (eg. 0.05) .HP \fB\-pseudoIntron\fR [0.0] .TP \fB\-pseudoInter\fR [0.0] .TP \fB\-min\-counts\fR [0] .HP \fB\-lcmask\fR [\-fragmentN] .TP \fB\-utr5\-length\fR [50] .TP \fB\-utr5\-offset\fR [10] .TP \fB\-utr3\-length\fR [50] .TP \fB\-utr3\-offset\fR [10] .TP \fB\-explicit\fR [250] .TP \fB\-min\-intron\fR [30] .TP \fB\-boost\fR (file of ID ) debian/mans/zoe-loop.10000644000000000000000000000137012237207531011755 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3. .TH ZOE-LOOP "1" "October 2013" "zoe-loop 2010-07-28" "User Commands" .SH NAME zoe-loop \- SNAP module zoe-loop .SH SYNOPSIS .B zoe\-loop <\fBtest\fR> [\fIiterations \- default 1000\fR] .SH OPTIONS .HP \fB\-all\fR .HP \fB\-Vec\fR, \fB\-IVec\fR, \fB\-FVec\fR, \fB\-TVec\fR, \fB\-Hash\fR \fB\-Xtree\fR .HP \fB\-Feature\fR, \fB\-FeatureVec\fR .HP \fB\-FastaFile\fR, \fB\-DNA\fR, \fB\-Protein\fR, \fB\-Alignment\fR \fB\-CDS\fR \fB\-Palign\fR .HP \fB\-Distribution\fR, \fB\-Duration\fR, \fB\-State\fR, \fB\-Transition\fR .PP The following tests are not part of \fB\-all\fR and require files .HP \fB\-FeatureTable\fR .HP \fB\-Model\fR, \fB\-Scanner\fR, \fB\-Counter\fR .HP \fB\-HMM\fR debian/mans/hmm-info.10000644000000000000000000000037512237207074011731 0ustar .TH HMM-INFO "1" "October 2013" "hmm-info 2010-07-28" "User Commands" .SH NAME hmm-info \- SNAP module hmm-info .SH SYNOPSIS .B hmm\-info [\fIoptions\fR] <\fBhmm file\fR> .SH OPTIONS .HP \fB\-models\fR .HP \fB\-general\fR .HP \fB\-durations\fR debian/docs0000644000000000000000000000001111576505436010045 0ustar 00README debian/upstream0000644000000000000000000000050412214301244010741 0ustar Name: SNAP Reference: Author: Ian Korf Title: Gene finding in novel Genomes Journal: BMC Bioinformatics Year: 2004 Volume: 5 Pages: 59 PMID: 15144565 DOI: 10.1186/1471-2105-5-59 URL: http://www.biomedcentral.com/1471-2105/5/59/abstract eprint: http://www.biomedcentral.com/content/pdf/1471-2105-5-59.pdf