[med-svn] r13093 - in trunk/packages/vcftools/trunk/debian: . patches
Thorsten Alteholz
alteholz at alioth.debian.org
Sun Feb 24 15:33:43 UTC 2013
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 <domibel at debian.org> Tue, 19 Feb 2013 14:18:25 -0500
+ -- Thorsten Alteholz <debian at 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
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