This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository varscan.
commit 1aa6e7173a4b5ba0fbb06088141e7f6d317e8958 Author: Andreas Tille <[email protected]> Date: Thu Apr 17 10:51:58 2014 +0200 Also fix usage in user manual --- debian/docs | 1 + debian/get-manual | 4 ++-- debian/using-varscan.txt | 52 ++++++++++++++++++++++++------------------------ 3 files changed, 29 insertions(+), 28 deletions(-) diff --git a/debian/docs b/debian/docs new file mode 100644 index 0000000..9e4d8fb --- /dev/null +++ b/debian/docs @@ -0,0 +1 @@ +debian/*.txt diff --git a/debian/get-manual b/debian/get-manual index 27d123d..1639009 100755 --- a/debian/get-manual +++ b/debian/get-manual @@ -6,8 +6,8 @@ cat >$OUT <<EOT VarScan User's Manual ===================== EOT -sed "1,/^VarScan User's Manual/d" $TMP >> $OUT - +sed -e "1,/^VarScan User's Manual/d" $TMP \ + -e 's/USAGE: java -jar VarScan.jar/USAGE: varscan/' >> $OUT OUT=faq.txt w3m -dump http://varscan.sourceforge.net/support-faq.html > $TMP diff --git a/debian/using-varscan.txt b/debian/using-varscan.txt index 8d03809..fce853f 100644 --- a/debian/using-varscan.txt +++ b/debian/using-varscan.txt @@ -13,7 +13,7 @@ prior, see below. VarScan Documentation (v2.2.3 and later) - USAGE: java -jar VarScan.jar [COMMAND] [OPTIONS] + USAGE: varscan [COMMAND] [OPTIONS] COMMANDS: @@ -45,7 +45,7 @@ pileup2snp This command calls SNPs from a pileup file based on user-defined parameters: - USAGE: java -jar VarScan.jar pileup2snp [pileup file] OPTIONS + USAGE: varscan pileup2snp [pileup file] OPTIONS pileup file - The SAMtools pileup file OPTIONS: @@ -82,7 +82,7 @@ pileup2indel This command calls indels from a pileup file based on user-defined parameters: - USAGE: java -jar VarScan.jar pileup2indel [pileup file] OPTIONS + USAGE: varscan pileup2indel [pileup file] OPTIONS pileup file - The SAMtools pileup file OPTIONS: @@ -120,7 +120,7 @@ pileup2cns This command makes consensus calls (SNP/Indel/Reference) from a pileup file based on user-defined parameters: - USAGE: java -jar VarScan.jar pileup2cns [pileup file] OPTIONS + USAGE: varscan pileup2cns [pileup file] OPTIONS pileup file - The SAMtools pileup file OPTIONS: @@ -156,7 +156,7 @@ mpileup2snp This command calls SNPs from an mpileup file based on user-defined parameters: - USAGE: java -jar VarScan.jar mpileup2snp [mpileup file] OPTIONS + USAGE: varscan mpileup2snp [mpileup file] OPTIONS mpileup file - The SAMtools mpileup file OPTIONS: @@ -208,7 +208,7 @@ mpileup2indel This command calls indels from a mpileup file based on user-defined parameters: - USAGE: java -jar VarScan.jar mpileup2indel [mpileup file] OPTIONS + USAGE: varscan mpileup2indel [mpileup file] OPTIONS mpileup file - The SAMtools mpileup file OPTIONS: @@ -261,7 +261,7 @@ mpileup2cns This command makes consensus calls (SNP/Indel/Reference) from a mpileup file based on user-defined parameters: - USAGE: java -jar VarScan.jar mpileup2cns [mpileup file] OPTIONS + USAGE: varscan mpileup2cns [mpileup file] OPTIONS mpileup file - The SAMtools mpileup file OPTIONS: @@ -314,7 +314,7 @@ somatic This command calls variants and identifies their somatic status (Germline/LOH/ Somatic) using pileup files from a matched tumor-normal pair. - USAGE: java -jar VarScan.jar somatic [normal_pileup] [tumor_pileup] [output] OPTIONS + USAGE: varscan somatic [normal_pileup] [tumor_pileup] [output] OPTIONS normal_pileup - The SAMtools pileup file for Normal tumor_pileup - The SAMtools pileup file for Tumor output - Output base name for SNP and indel output @@ -322,7 +322,7 @@ Somatic) using pileup files from a matched tumor-normal pair. You can also give it a single mpileup file with normal and tumor data. - USAGE: java -jar VarScan.jar somatic [normal-tumor.mpileup] [output] --mpileup 1 OPTIONS + USAGE: varscan somatic [normal-tumor.mpileup] [output] --mpileup 1 OPTIONS normal-tumor.mpileup - The SAMtools mpileup file with normal and then tumor output - Output base name for SNP and indel output @@ -397,7 +397,7 @@ copynumber This command calls variants and identifies their somatic status (Germline/LOH/ Somatic) using pileup files from a matched tumor-normal pair. - USAGE: java -jar VarScan.jar copynumber [normal_pileup] [tumor_pileup] [output] OPTIONS + USAGE: varscan copynumber [normal_pileup] [tumor_pileup] [output] OPTIONS normal_pileup - The SAMtools pileup file for Normal tumor_pileup - The SAMtools pileup file for Tumor output - Output base name for SNP and indel output @@ -405,7 +405,7 @@ Somatic) using pileup files from a matched tumor-normal pair. You can also give it a single mpileup file with normal and tumor data. - USAGE: java -jar VarScan.jar copynumber [normal-tumor.mpileup] [output] --mpileup 1 OPTIONS + USAGE: varscan copynumber [normal-tumor.mpileup] [output] --mpileup 1 OPTIONS normal-tumor.mpileup - The SAMtools mpileup file with normal and then tumor output - Output base name for SNP and indel output @@ -453,7 +453,7 @@ This command filters variants in a file by coverage, supporting reads, variant frequency, or average base quality. It is for use with output from pileup2snp or pileup2indel. - USAGE: java -jar VarScan.jar filter [variants file] OPTIONS + USAGE: varscan filter [variants file] OPTIONS variants file - A file of SNP or indel calls from VarScan pileup2snp or pileup2indel OPTIONS: @@ -477,7 +477,7 @@ soft-trimming, and other factors when deciding whether or not to filter a variant. See the VarScan 2 publication (Koboldt et al, Genome Research, Feb 2012) for details. - USAGE: java -jar VarScan.jar somaticFilter [mutations file] OPTIONS + USAGE: varscan somaticFilter [mutations file] OPTIONS mutations file - A file of SNVs from VarScan somatic OPTIONS: @@ -495,7 +495,7 @@ limit This command limits variants in a file to a set of positions or regions -USAGE: java -jar VarScan.jar limit [infile] OPTIONS +USAGE: varscan limit [infile] OPTIONS infile - A file of chromosome-positions, tab-delimited OPTIONS @@ -509,7 +509,7 @@ readcounts This command reports the read counts for each base at positions in a pileup file -USAGE: java -jar VarScan.jar readcounts [pileup file] OPTIONS +USAGE: varscan readcounts [pileup file] OPTIONS pileup file - The SAMtools pileup file OPTIONS: @@ -523,7 +523,7 @@ compare This command performs set-comparison operations on two files of variants. -USAGE: java -jar VarScan.jar compare [file1] [file2] [type] [output] OPTIONS +USAGE: varscan compare [file1] [file2] [type] [output] OPTIONS file1 - A file of chromosome-positions, tab-delimited file2 - A file of chromosome-positions, tab-delimited type - Type of comparison [intersect|merge|unique1|unique2] @@ -539,7 +539,7 @@ For detailed usage information, see the VarScan JavaDoc. VarScan Documentation (v2.2.2 and before) - USAGE: java -jar VarScan.jar [COMMAND] [OPTIONS] + USAGE: varscan [COMMAND] [OPTIONS] COMMANDS pileup2snp [pileup file] @@ -558,7 +558,7 @@ pileup2snp This command calls SNPs from a pileup file based on user-defined parameters: - USAGE: java -jar VarScan.jar pileup2snp [pileup file] OPTIONS + USAGE: varscan pileup2snp [pileup file] OPTIONS pileup file - The SAMtools pileup file OPTIONS: @@ -588,7 +588,7 @@ pileup2indel This command calls indels from a pileup file based on user-defined parameters: - USAGE: java -jar VarScan.jar pileup2indel [pileup file] OPTIONS + USAGE: varscan pileup2indel [pileup file] OPTIONS pileup file - The SAMtools pileup file OPTIONS: @@ -619,7 +619,7 @@ pileup2cns This command makes consensus calls (SNP/Indel/Reference) from a pileup file based on user-defined parameters: - USAGE: java -jar VarScan.jar pileup2cns [pileup file] OPTIONS + USAGE: varscan pileup2cns [pileup file] OPTIONS pileup file - The SAMtools pileup file OPTIONS: @@ -650,7 +650,7 @@ somatic This command calls variants and identifies their somatic status (Germline/LOH/ Somatic) using pileup files from a matched tumor-normal pair. - USAGE: java -jar VarScan.jar somatic [normal_pileup] [tumor_pileup] [output] OPTIONS + USAGE: varscan somatic [normal_pileup] [tumor_pileup] [output] OPTIONS normal_pileup - The SAMtools pileup file for Normal tumor_pileup - The SAMtools pileup file for Tumor output - Output base name for SNP and indel output @@ -689,7 +689,7 @@ filter This command filters variants in a file by coverage, supporting reads, variant frequency, or average base quality - USAGE: java -jar VarScan.jar filter [variants file] OPTIONS + USAGE: varscan filter [variants file] OPTIONS variants file - A file of SNP or indel calls from VarScan OPTIONS: @@ -705,7 +705,7 @@ somaticFilter This command filters somatic mutation calls to remove clusters of false positives and SNV calls near indels. - USAGE: java -jar VarScan.jar somaticFilter [mutations file] OPTIONS + USAGE: varscan somaticFilter [mutations file] OPTIONS mutations file - A file of SNVs from VarScan somatic OPTIONS: @@ -723,7 +723,7 @@ limit This command limits variants in a file to a set of positions or regions -USAGE: java -jar VarScan.jar limit [infile] OPTIONS +USAGE: varscan limit [infile] OPTIONS infile - A file of chromosome-positions, tab-delimited OPTIONS @@ -737,7 +737,7 @@ readcounts This command reports the read counts for each base at positions in a pileup file -USAGE: java -jar VarScan.jar readcounts [pileup file] OPTIONS +USAGE: varscan readcounts [pileup file] OPTIONS pileup file - The SAMtools pileup file OPTIONS: @@ -751,7 +751,7 @@ compare This command performs set-comparison operations on two files of variants. -USAGE: java -jar VarScan.jar compare [file1] [file2] [type] [output] OPTIONS +USAGE: varscan compare [file1] [file2] [type] [output] OPTIONS file1 - A file of chromosome-positions, tab-delimited file2 - A file of chromosome-positions, tab-delimited type - Type of comparison [intersect|merge|unique1|unique2] -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/varscan.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
