[med-svn] [varscan] 01/02: Also fix usage in user manual
Andreas Tille
tille at debian.org
Thu Apr 17 09:07:55 UTC 2014
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 <tille at debian.org>
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]
--
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