Author: alteholz Date: 2013-02-24 15:33:43 +0000 (Sun, 24 Feb 2013) New Revision: 13093
Added: trunk/packages/vcftools/trunk/debian/fill-fs.1 trunk/packages/vcftools/trunk/debian/fill-ref-md5.1 trunk/packages/vcftools/trunk/debian/vcf-consensus.1 trunk/packages/vcftools/trunk/debian/vcf-contrast.1 trunk/packages/vcftools/trunk/debian/vcf-fix-ploidy.1 trunk/packages/vcftools/trunk/debian/vcf-indel-stats.1 trunk/packages/vcftools/trunk/debian/vcf-phased-join.1 trunk/packages/vcftools/trunk/debian/vcf-shuffle-cols.1 trunk/packages/vcftools/trunk/debian/vcf-tstv.1 trunk/packages/vcftools/trunk/debian/vcftools.lintian-overrides Modified: trunk/packages/vcftools/trunk/debian/changelog trunk/packages/vcftools/trunk/debian/manpages trunk/packages/vcftools/trunk/debian/patches/use-dpkg-buildflags.patch Log: preparation of new version Modified: trunk/packages/vcftools/trunk/debian/changelog =================================================================== --- trunk/packages/vcftools/trunk/debian/changelog 2013-02-24 15:31:06 UTC (rev 13092) +++ trunk/packages/vcftools/trunk/debian/changelog 2013-02-24 15:33:43 UTC (rev 13093) @@ -1,10 +1,16 @@ -vcftools (0.1.10+dfsg-1) UNRELEASED; urgency=low +vcftools (0.1.10+dfsg-1) unstable; urgency=low + [ Thorsten Alteholz ] + * add man pages for new scripts + * debian/patches/use-dpkg-buildflags.patch: add LDFLAGS to link stage + * debian/vcftools.lintian-overrides: false positive + + [ Dominique Belhachemi ] * New upstream version - * Updated debian/use-dpkg-buildflags.patch - * Removed debian/perl.patch (applied upstream) + * Updated debian/patches/use-dpkg-buildflags.patch + * Removed debian/patches/perl.patch (applied upstream) - -- Dominique Belhachemi <domi...@debian.org> Tue, 19 Feb 2013 14:18:25 -0500 + -- Thorsten Alteholz <deb...@alteholz.de> Sun, 24 Feb 2013 16:00:00 +0100 vcftools (0.1.9+dfsg-2) unstable; urgency=low Added: trunk/packages/vcftools/trunk/debian/fill-fs.1 =================================================================== --- trunk/packages/vcftools/trunk/debian/fill-fs.1 (rev 0) +++ trunk/packages/vcftools/trunk/debian/fill-fs.1 2013-02-24 15:33:43 UTC (rev 13093) @@ -0,0 +1,39 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1. +.TH FILL-FS "1" "February 2013" "fill-fs" "User Commands" +.SH NAME +fill-fs \- Annotate VCF with flanking sequence +.SH SYNOPSIS +.B fill-fs +[\fIOPTIONS\fR] \fIfile.vcf\fR +.SH DESCRIPTION +About: Annotate VCF with flanking sequence (INFO/FS tag) +.SH OPTIONS +.TP +\fB\-b\fR, \fB\-\-bed\-mask\fR <file> +Regions to mask (tabix indexed), multiple files can be given +.TP +\fB\-c\fR, \fB\-\-cluster\fR <int> +Do self\-masking of clustered variants within this range. +.TP +\fB\-l\fR, \fB\-\-length\fR <int> +Flanking sequence length [100] +.TP +\fB\-m\fR, \fB\-\-mask\-char\fR <char|lc> +The character to use or "lc" for lowercase. This option must preceed +\fB\-b\fR, \fB\-v\fR or \fB\-c\fR in order to take effect. With multiple files works +.IP +as a switch on the command line, see the example below [N] +.TP +\fB\-r\fR, \fB\-\-refseq\fR <file> +The reference sequence. +.TP +\fB\-v\fR, \fB\-\-vcf\-mask\fR <file> +Mask known variants in the flanking sequence, multiple files can be given (tabix indexed) +.TP +\fB\-h\fR, \-?, \fB\-\-help\fR +This help message. +.SS "Example:" +.IP +# Mask variants from the VCF file with N's and use lowercase for the bed file regions +fill\-fs file.vcf \fB\-v\fR mask.vcf \fB\-m\fR lc \fB\-b\fR mask.bed +.IP Added: trunk/packages/vcftools/trunk/debian/fill-ref-md5.1 =================================================================== --- trunk/packages/vcftools/trunk/debian/fill-ref-md5.1 (rev 0) +++ trunk/packages/vcftools/trunk/debian/fill-ref-md5.1 2013-02-24 15:33:43 UTC (rev 13093) @@ -0,0 +1,31 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1. +.TH FILL-REF-MD5 "1" "February 2013" "fill-ref-md5" "User Commands" +.SH NAME +fill-ref-md5 \- computes MD5 sum of the reference sequence +.SH SYNOPSIS +.B fill-ref-md5 +[\fIOPTIONS\fR] \fIin.vcf.gz out.vcf.gz\fR +.SH DESCRIPTION +About: The script computes MD5 sum of the reference sequence and inserts +.IP +\&'reference' and 'contig' tags into header as recommended by VCFv4.1. +The VCF file must be compressed and tabix indexed, as it takes advantage +of the lightning fast tabix reheader functionality. +.SH OPTIONS +.TP +\fB\-d\fR, \fB\-\-dictionary\fR <file> +Where to read/write computed MD5s. Opened in append mode, existing records are not touched. +.TP +\fB\-i\fR, \fB\-\-info\fR <AS:xx,SP:xx,TX:xx> +Optional info on reference assembly (AS), species (SP), taxonomy (TX) +.TP +\fB\-r\fR, \fB\-\-refseq\fR <file> +The reference sequence in fasta format indexed by samtools faidx +.TP +\fB\-h\fR, \-?, \fB\-\-help\fR +This help message. +.SH EXAMPLES +.TP +fill\-ref\-md5 \-i AS:NCBIM37,SP:"Mus\e Musculus" \-r NCBIM37_um.fa +\-d NCBIM37_um.fa.dict in.vcf.gz out.vcf.gz +.IP Modified: trunk/packages/vcftools/trunk/debian/manpages =================================================================== --- trunk/packages/vcftools/trunk/debian/manpages 2013-02-24 15:31:06 UTC (rev 13092) +++ trunk/packages/vcftools/trunk/debian/manpages 2013-02-24 15:33:43 UTC (rev 13093) @@ -14,4 +14,12 @@ debian/fill-aa.1 debian/fill-an-ac.1 debian/fill-rsIDs.1 - +debian/fill-fs.1 +debian/fill-ref-md5.1 +debian/vcf-consensus.1 +debian/vcf-contrast.1 +debian/vcf-fix-ploidy.1 +debian/vcf-indel-stats.1 +debian/vcf-phased-join.1 +debian/vcf-shuffle-cols.1 +debian/vcf-tstv.1 Modified: trunk/packages/vcftools/trunk/debian/patches/use-dpkg-buildflags.patch =================================================================== --- trunk/packages/vcftools/trunk/debian/patches/use-dpkg-buildflags.patch 2013-02-24 15:31:06 UTC (rev 13092) +++ trunk/packages/vcftools/trunk/debian/patches/use-dpkg-buildflags.patch 2013-02-24 15:33:43 UTC (rev 13093) @@ -2,9 +2,11 @@ Date: Sat, 12 May 2012 09:31:58 +0200 Description: Enable propagation of hardening flags ---- vcftools-0.1.10+dfsg.orig/cpp/Makefile -+++ vcftools-0.1.10+dfsg/cpp/Makefile -@@ -11,7 +11,7 @@ ifndef VCFTOOLS_PCA +Index: vcftools_0.1.10/cpp/Makefile +=================================================================== +--- vcftools_0.1.10.orig/cpp/Makefile 2013-02-24 16:09:58.000000000 +0100 ++++ vcftools_0.1.10/cpp/Makefile 2013-02-24 16:10:22.000000000 +0100 +@@ -11,7 +11,7 @@ VCFTOOLS_PCA = 0 endif # Compiler flags @@ -13,7 +15,16 @@ #CPPFLAGS = -g # Included libraries (zlib) LIB = -lz -@@ -44,8 +44,8 @@ endif +@@ -35,7 +35,7 @@ + endif + + vcftools: $(OBJS) +- $(CPP) $(OBJS) -o vcftools $(LIB) ++ $(CPP) $(OBJS) $(LDFLAGS) -o vcftools $(LIB) + ifdef BINDIR + cp $(CURDIR)/$@ $(BINDIR)/$@ + endif +@@ -44,8 +44,8 @@ -include $(OBJS:.o=.d) %.o: %.cpp Added: trunk/packages/vcftools/trunk/debian/vcf-consensus.1 =================================================================== --- trunk/packages/vcftools/trunk/debian/vcf-consensus.1 (rev 0) +++ trunk/packages/vcftools/trunk/debian/vcf-consensus.1 2013-02-24 15:33:43 UTC (rev 13093) @@ -0,0 +1,14 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1. +.TH VCF-CONSENSUS "1" "February 2013" "vcf-consensus" "User Commands" +.SH NAME +vcf-consensus \- vcf-consensus +.SH SYNOPSIS +.B cat +\fIref.fa | vcf-consensus \fR[\fIOPTIONS\fR] \fIin.vcf.gz > out.txt\fR +.SH OPTIONS +.TP +\fB\-h\fR, \-?, \fB\-\-help\fR +This help message. +.HP +\fB\-s\fR, \fB\-\-sample\fR <name> +.IP Added: trunk/packages/vcftools/trunk/debian/vcf-contrast.1 =================================================================== --- trunk/packages/vcftools/trunk/debian/vcf-contrast.1 (rev 0) +++ trunk/packages/vcftools/trunk/debian/vcf-contrast.1 2013-02-24 15:33:43 UTC (rev 13093) @@ -0,0 +1,39 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1. +.TH VCF-CONTRAST "1" "February 2013" "vcf-contrast" "User Commands" +.SH NAME +vcf-contrast \- finds differences amongst samples +.SH SYNOPSIS +.B vcf-contrast +\fI+<list> -<list> \fR[\fIOPTIONS\fR] \fIfile.vcf.gz\fR +.SH DESCRIPTION +About: Finds differences amongst samples adding NOVEL* annotation to INFO field. +.SH OPTIONS +.TP ++<list> +List of samples where unique variant is expected +.TP +\-<list> +List of background samples +.TP +\fB\-d\fR, \fB\-\-min\-DP\fR <int> +Minimum depth across all \-<list> samples +.TP +\fB\-f\fR, \fB\-\-apply\-filters\fR +Skip sites with FILTER column different from PASS or "." +.TP +\fB\-n\fR, \fB\-\-novel\-sites\fR +Print only records with novel genotypes +.TP +\fB\-h\fR, \-?, \fB\-\-help\fR +This help message. +.SS "Example:" +.IP +# Test if any of the samples A,B is different from all C,D,E +vcf\-contrast +A,B \fB\-C\fR,D,E \fB\-m\fR file.vcf.gz +.IP +# Same as above but printing only sites with novel variants and table output +vcf\-contrast \fB\-n\fR +A,B \fB\-C\fR,D,E \fB\-m\fR file.vcf.gz | vcf\-query \fB\-f\fR '%CHROM %POS\et%INFO/NOVELTY\et%INFO/NOVELAL\et%INFO/NOVELGT[\et%SAMPLE %GTR %PL]\en' +.IP +# Similar to above but require minimum mapping quality of 20 +vcf\-annotate \fB\-f\fR MinMQ=20 file.vcf.gz | vcf\-contrast +A,B,C \fB\-D\fR,E,F \fB\-f\fR +.IP Added: trunk/packages/vcftools/trunk/debian/vcf-fix-ploidy.1 =================================================================== --- trunk/packages/vcftools/trunk/debian/vcf-fix-ploidy.1 (rev 0) +++ trunk/packages/vcftools/trunk/debian/vcf-fix-ploidy.1 2013-02-24 15:33:43 UTC (rev 13093) @@ -0,0 +1,52 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1. +.TH VCF-FIX-PLOIDY "1" "February 2013" "vcf-fix-ploidy" "User Commands" +.SH NAME +vcf-fix-ploidy \- vcf-fix-ploidy +.SH SYNOPSIS +.B cat +\fIbroken.vcf | vcf-fix-ploidy \fR[\fIOPTIONS\fR] \fI> fixed.vcf\fR +.SH OPTIONS +.TP +\fB\-a\fR, \fB\-\-assumed\-sex\fR <sex> +M or F, required if the list is not complete in \fB\-s\fR +.TP +\fB\-l\fR, \fB\-\-fix\-likelihoods\fR +Add or remove het likelihoods (not the default behaviour) +.TP +\fB\-p\fR, \fB\-\-ploidy\fR <file> +Ploidy definition. The default is shown below. +.TP +\fB\-s\fR, \fB\-\-samples\fR <file> +List of sample sexes (sample_name [MF]). +.TP +\fB\-h\fR, \-?, \fB\-\-help\fR +This help message. +.SS "Default ploidy definition:" +.IP +ploidy => +{ +.IP +X => +[ +.IP +# The pseudoautosomal regions 60,001\-2,699,520 and 154,931,044\-155,270,560 with the ploidy 2 +{ from=>1, to=>60_000, M=>1 }, +{ from=>2_699_521, to=>154_931_043, M=>1 }, +.IP +], +Y => +[ +.IP +# No chrY in females and one copy in males +{ from=>1, to=>59_373_566, M=>1, F=>0 }, +.IP +], +MT => +[ +.IP +# Haploid MT in males and females +{ from=>1, to => 16_569, M=>1, F=>1 }, +.IP +], +.IP +} Added: trunk/packages/vcftools/trunk/debian/vcf-indel-stats.1 =================================================================== --- trunk/packages/vcftools/trunk/debian/vcf-indel-stats.1 (rev 0) +++ trunk/packages/vcftools/trunk/debian/vcf-indel-stats.1 2013-02-24 15:33:43 UTC (rev 13093) @@ -0,0 +1,19 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1. +.TH VCF-INDEL-STATS "1" "February 2013" "vcf-indel-stats" "User Commands" +.SH NAME +vcf-indel-stats \- vcf-indel-stat +.SH SYNOPSIS +.B vcf-indel-stats +[\fIOPTIONS\fR] \fI< in.vcf > out.txt\fR +.SH DESCRIPTION +About: Currently calculates in\-frame ratio. +.SH OPTIONS +.TP +\fB\-h\fR, \-?, \fB\-\-help\fR +This help message. +.TP +\fB\-e\fR, \fB\-\-exons\fR <file> +Tab\-separated file with exons (chr,from,to; 1\-based, inclusive) +.HP +\fB\-v\fR, \fB\-\-verbose\fR +.IP Added: trunk/packages/vcftools/trunk/debian/vcf-phased-join.1 =================================================================== --- trunk/packages/vcftools/trunk/debian/vcf-phased-join.1 (rev 0) +++ trunk/packages/vcftools/trunk/debian/vcf-phased-join.1 2013-02-24 15:33:43 UTC (rev 13093) @@ -0,0 +1,28 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1. +.TH VCF-PHASED-JOIN "1" "February 2013" "vcf-phased-join" "User Commands" +.SH NAME +vcf-phased-join \- take multiple overlapping pre\-phased chunks and concatenates them into one VCF +.SH SYNOPSIS +.B vcf-phased-join +[\fIOPTIONS\fR] \fIA.vcf B.vcf C.vcf\fR +.SH DESCRIPTION +About: The script takes multiple overlapping pre\-phased chunks and concatenates them into one VCF +.IP +using heterozygous calls from the overlaps to determine correct phase. +.SH OPTIONS +.TP +\fB\-j\fR, \fB\-\-min\-join\-quality\fR <num> +Quality threshold for gluing the pre\-phased blocks together [10] +.TP +\fB\-l\fR, \fB\-\-list\fR <file> +List of VCFs to join. +.TP +\fB\-o\fR, \fB\-\-output\fR <file> +Output file name. When "\-" is supplied, STDOUT and STDERR will be used +.TP +\fB\-q\fR, \fB\-\-min\-PQ\fR <num> +Break pre\-phased segments if PQ value is lower in input VCFs [0.6] +.TP +\fB\-h\fR, \-?, \fB\-\-help\fR +This help message +.IP Added: trunk/packages/vcftools/trunk/debian/vcf-shuffle-cols.1 =================================================================== --- trunk/packages/vcftools/trunk/debian/vcf-shuffle-cols.1 (rev 0) +++ trunk/packages/vcftools/trunk/debian/vcf-shuffle-cols.1 2013-02-24 15:33:43 UTC (rev 13093) @@ -0,0 +1,17 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1. +.TH VCF-SHUFFLE-COLS "1" "February 2013" "vcf-shuffle-cols" "User Commands" +.SH NAME +vcf-shuffle-cols \- reorder columns +.SH SYNOPSIS +.B vcf-shuffle-cols +[\fIOPTIONS\fR] \fI-t template.vcf.gz file.vcf.gz > out.vcf\fR +.SH DESCRIPTION +About: Reorder columns to match the order in the template VCF. +.SH OPTIONS +.TP +\fB\-t\fR, \fB\-\-template\fR <file> +The file with the correct order of the columns. +.TP +\fB\-h\fR, \-?, \fB\-\-help\fR +This help message. +.IP Added: trunk/packages/vcftools/trunk/debian/vcf-tstv.1 =================================================================== --- trunk/packages/vcftools/trunk/debian/vcf-tstv.1 (rev 0) +++ trunk/packages/vcftools/trunk/debian/vcf-tstv.1 2013-02-24 15:33:43 UTC (rev 13093) @@ -0,0 +1,12 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1. +.TH VCF-TSTV "1" "February 2013" "vcf-tstv" "User Commands" +.SH NAME +vcf-tstv \- vcf-tstv +.SH SYNOPSIS +.B cat +\fIfile.vcf | vcf-tstv\fR +.SH OPTIONS +.TP +\fB\-h\fR, \-?, \fB\-\-help\fR +This help message. +.IP Added: trunk/packages/vcftools/trunk/debian/vcftools.lintian-overrides =================================================================== --- trunk/packages/vcftools/trunk/debian/vcftools.lintian-overrides (rev 0) +++ trunk/packages/vcftools/trunk/debian/vcftools.lintian-overrides 2013-02-24 15:33:43 UTC (rev 13093) @@ -0,0 +1,2 @@ +# the compiler flags are used +vcftools: hardening-no-fortify-functions usr/bin/vcftools _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit