[med-svn] [SCM] gmap branch, master, updated. upstream/2013-07-20-19-gcea86c7
Andreas Tille
tille at debian.org
Fri Aug 2 13:34:33 UTC 2013
The following commit has been merged in the master branch:
commit cea86c763455631a83195f2aca75483f55dcc830
Author: Andreas Tille <tille at debian.org>
Date: Fri Aug 2 15:29:22 2013 +0200
Fetch some of the `hyphen-used-as-minus-sign` lintian issues. Some false positives and some others might remain
diff --git a/debian/gmap.1 b/debian/gmap.1
index 48194b3..b8c6080 100644
--- a/debian/gmap.1
+++ b/debian/gmap.1
@@ -137,11 +137,11 @@ greater than this value (default 0.90)
.TP
\fB--cmetdir\fR=\fISTRING\fR
Directory for methylcytosine index files (created using cmetindex)
-(default is location of genome index files specified using -D, -V, and -d)
+(default is location of genome index files specified using \-D, \-V, and \-d)
.TP
\fB--atoidir\fR=\fISTRING\fR
Directory for A-to-I RNA editing index files (created using atoiindex)
-(default is location of genome index files specified using -D, -V, and -d)
+(default is location of genome index files specified using \-D, \-V, and \-d)
.TP
\fB--mode\fR=\fISTRING\fR
Alignment mode: standard (default), cmet-stranded, cmet-nonstranded,
@@ -179,7 +179,7 @@ Print protein sequence (cDNA)
Print protein sequence (genomic)
.TP
\fB\-f\fR, \fB\-\-format\fR=\fIINT\fR
-Other format for output (also note the -A and -S options and other
+Other format for output (also note the \-A and \-S options and other
options listed under Output types):
psl (or 1)= PSL (BLAT) format,
gff3_gene (or 2)= GFF3 gene format,
@@ -233,7 +233,7 @@ previously using snpindex) for reporting output
.TP
\fB\-\-split-output\fR=\fISTRING\fR
Basename for multiple-file output, separately for nomapping,
-uniq, mult, (and chimera, if --chimera-margin is selected)
+uniq, mult, (and chimera, if \-\-chimera\-margin is selected)
.TP
\fB--output-buffer-size\fR=\fIINT\fR
Buffer size, in queries, for output thread (default 1000). When the
@@ -278,8 +278,8 @@ Options for quality scores
.TP
\fB--quality-protocol\fR=\fISTRING\fR
Protocol for input quality scores. Allowed values:
- illumina (ASCII 64-126) (equivalent to -J 64 -j -31)
- sanger (ASCII 33-126) (equivalent to -J 33 -j 0)
+ illumina (ASCII 64-126) (equivalent to \-J 64 \-j -31)
+ sanger (ASCII 33-126) (equivalent to \-J 33 \-j 0)
Default is sanger (no quality print shift)
SAM output files should have quality scores in sanger protocol.
diff --git a/debian/gsnap.1 b/debian/gsnap.1
index 34011a4..f22267e 100644
--- a/debian/gsnap.1
+++ b/debian/gsnap.1
@@ -121,7 +121,7 @@ Note that this default value may not be low enough if you want to
obtain terminal alignments for very short reads, although such reads
probably don't have enough specificity for terminal alignments anyway.
To turn off terminal alignments, set this to a high value, greater
-than the value for --max-mismatches.
+than the value for \-\-max\-mismatches.
.TP
\fB\-i\fR, \fB\-\-indel\-penalty\fR=\fIINT\fR
Penalty for an indel (default 2).
@@ -167,7 +167,7 @@ will give false positive indels at the ends of reads
.TP
\fB\-V\fR, \fB\-\-snpsdir\fR=\fISTRING\fR
Directory for SNPs index files (created using snpindex) (default is
-location of genome index files specified using -D and -d)
+location of genome index files specified using \-D and \-d)
.TP
\fB\-v\fR, \fB\-\-use\-snps\fR=\fISTRING\fR
Use database containing known SNPs (in <STRING>.iit, built
@@ -175,12 +175,12 @@ previously using snpindex) for tolerance to SNPs
.TP
\fB\-\-cmetdir\fR=\fISTRING\fR
Directory for methylcytosine index files (created using cmetindex)
-default is location of genome index files specified using -D, -V, and -d)
+default is location of genome index files specified using \-D, \-V, and \-d)
.TP
\fB--atoidir\fR=\fISTRING\fR
Directory for A-to-I RNA editing index files (created using atoiindex)
-(default is location of genome index files specified using -D, -V, and
--d)
+(default is location of genome index files specified using \-D, \-V, and
+\-d)
.TP
\fB--mode\fR=\fISTRING\fR
Alignment mode: standard (default), cmet-stranded, cmet-nonstranded,
@@ -189,17 +189,17 @@ to have previously run the cmetindex or atoiindex programs on the genome
.TP
\fB--tallydir\fR=\fISTRING\fR
Directory for tally IIT file to resolve concordant multiple results
-(default is location of genome index files specified using -D and -d).
-Note: can just give full path name to --use\-tally instead.
+(default is location of genome index files specified using \-D and \-d).
+Note: can just give full path name to \-\-use\-tally instead.
.TP
\fB--use-tally\fR=\fISTRING\fR
Use this tally IIT file to resolve concordant multiple results
.TP
\fB--runlengthdir\fR=\fISTRING\fR
Directory for runlength IIT file to resolve concordant multiple
-results (default is location of genome index files specified using -D
-and -d).
-Note: can just give full path name to --use\-runlength instead.
+results (default is location of genome index files specified using \-D
+and \-d).
+Note: can just give full path name to \-\-use\-runlength instead.
.TP
\fB--use-runlength\fR=\fISTRING\fR
Use this runlength IIT file to resolve concordant multiple results
@@ -222,15 +222,15 @@ of both ends if paired-end) exceeds this value (default 5)
.TP
\fB--max-gmap-pairsearch\fR=\fIINT\fR
Perform GMAP pairsearch on nearby genomic regions up to this many
-many candidate ends (default 10). Requires pairsearch in --gmap-mode
+many candidate ends (default 10). Requires pairsearch in \-\-gmap\-mode
.TP
\fB--max-gmap-terminal\fR=\fIINT\fR
Perform GMAP terminal on nearby genomic regions up to this many
-candidate ends (default 5). Requires terminal in --gmap-mode
+candidate ends (default 5). Requires terminal in \-\-gmap\-mode
.TP
\fB--max-gmap-improvement\fR=\fIINT\fR
Perform GMAP improvement on nearby genomic regions up to this many
-candidate ends (default 5). Requires improve in --gmap-mode
+candidate ends (default 5). Requires improve in \-\-gmap\-mode
.TP
\fB--microexon-spliceprob\fR=\fIFLOAT\fR
Allow microexons only if one of the splice site probabilities is
@@ -244,9 +244,9 @@ Look for novel splicing (0=no (default), 1=yes)
.TP
\fB--splicingdir\fR=\fISTRING\fR
Directory for splicing involving known sites or known introns,
-as specified by the -s or --use-splicing flag (default is
-directory computed from -D and -d flags).
-Note: can just give full pathname to the -s flag instead.
+as specified by the \-s or \-\-use\-splicing flag (default is
+directory computed from \-D and \-d flags).
+Note: can just give full pathname to the \-s flag instead.
.TP
\fB\-s\fR, \fB--use-splicing\fR=\fISTRING\fR
Look for splicing involving known sites or known introns
@@ -257,8 +257,8 @@ known introns
\fB--ambig-splice-noclip\fR
For ambiguous known splicing at ends of the read, do not clip at the
splice site, but extend instead into the intron. This flag makes
-sense only if you provide the --use-splicing flag, and you are trying
-to eliminate all soft clipping with --trim-mismatch-score=0
+sense only if you provide the \-\-use\-splicing flag, and you are trying
+to eliminate all soft clipping with \-\-trim\-mismatch\-score=0
.TP
\fB\-w\fR, \fB\-\-localsplicedist\fR=\fIINT\fR
Definition of local novel splicing event (default 200000)
@@ -268,7 +268,7 @@ Penalty for a local splice (default 0). Counts against mismatches allowed
.TP
\fB\-E\fR, \fB\-\-distant\-splice\-penalty\fR=\fIINT\fR
Penalty for a distant splice (default 1). A distant splice is one where
-the intron length exceeds the value of -w, or --localsplicedist, or is an
+the intron length exceeds the value of \-w, or \-\-localsplicedist, or is an
inversion, scramble, or translocation between two different chromosomes
Counts against mismatches allowed
.TP
@@ -278,8 +278,8 @@ allowed is the value of -k, or kmer size)
.TP
\fB-l,\fR \fB\-\-shortend\-splice\-endlength\fR=\fIINT\fR
Minimum length at end required for short-end spliced alignments (default 2)
-but unless known splice sites are provided with the -s flag, GSNAP may still
-need the end length to be the value of -k, or kmer size to find a given splice
+but unless known splice sites are provided with the \-s flag, GSNAP may still
+need the end length to be the value of \-k, or kmer size to find a given splice
.TP
\fB\-\-distant\-splice\-identity\fR=\fIFLOAT\fR
Minimum identity at end required for distant spliced alignments (default 0.95)
@@ -300,12 +300,12 @@ Options for paired\-end reads
.TP
\fB\-\-pairmax-dna\fR=\fIINT\fR
Max total genomic length for DNA-Seq paired reads, or other reads
-without splicing (default 1000). Used if -N or -s is not specified.
+without splicing (default 1000). Used if \-N or \-s is not specified.
.TP
\fB\-\-pairmax\-rna\fR=\fIINT\fR
Max total genomic length for RNA-Seq paired reads, or other reads
-that could have a splice (default 200000). Used if -N or -s is specified.
-Should probably match the value for -w, --localsplicedist.
+that could have a splice (default 200000). Used if \-N or \-s is specified.
+Should probably match the value for \-w, \-\-localsplicedist.
.TP
\fB--pairexpect\fR=\fIINT\fR
Expected paired-end length, used for calling splices in medial part of
@@ -320,8 +320,8 @@ Options for quality scores
\fB\-\-quality\-protocol\fR=\fISTRING\fR
Protocol for input quality scores. Allowed values:
- illumina (ASCII 64-126) (equivalent to -J 64 -j -31)
- sanger (ASCII 33-126) (equivalent to -J 33 -j 0)
+ illumina (ASCII 64-126) (equivalent to \-J 64 \-j -31)
+ sanger (ASCII 33-126) (equivalent to \-J 33 \-j 0)
Default is sanger (no quality print shift)
SAM output files should have quality scores in sanger protocol
--
Align mRNA and EST sequences to a genome
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