[med-svn] [SCM] gmap branch, master, updated. upstream/2011-03-11-21-ge21796d
Shaun Jackman
sjackman at debian.org
Tue Aug 23 21:55:00 UTC 2011
The following commit has been merged in the master branch:
commit e21796d88ba8cf78ddbb3c851e412329ee96b25b
Author: Shaun Jackman <sjackman at debian.org>
Date: Tue Aug 23 14:54:38 2011 -0700
New upstream release.
diff --git a/debian/changelog b/debian/changelog
index 9cb0e8c..c3c12ac 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+gmap (2011-08-15-1) unstable; urgency=low
+
+ * New upstream release.
+ * Bump Standards-Version to 3.9.2.
+
+ -- Shaun Jackman <sjackman at debian.org> Tue, 23 Aug 2011 10:45:46 -0700
+
gmap (2011-03-11-1) unstable; urgency=low
* New upstream release.
diff --git a/debian/control b/debian/control
index 12fa327..c11fbfd 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
DM-Upload-Allowed: yes
Uploaders: Shaun Jackman <sjackman at debian.org>
Build-Depends: debhelper (>= 7.0.50~), autotools-dev
-Standards-Version: 3.9.1
+Standards-Version: 3.9.2
Homepage: http://research-pub.gene.com/gmap/
Vcs-Git: git://git.debian.org/git/debian-med/gmap.git
Vcs-Browser: http://git.debian.org/?p=debian-med/gmap.git
diff --git a/debian/copyright b/debian/copyright
index 23f323b..465e2a2 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -3,7 +3,7 @@ Name: GMAP
Maintainer: Thomas Wu <twu at gene.com>, Colin K. Watanabe <ckw at gene.com>
Source: http://research-pub.gene.com/gmap/
-Copyright: 2005 Genentech, Inc.
+Copyright: 2011 Genentech, Inc.
License: other
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
@@ -43,7 +43,7 @@ License: LGPL-2.1+
See `/usr/share/common-licenses/LGPL'.
Files: debian/*
-Copyright: 2010 Shaun Jackman <sjackman at debian.org>
+Copyright: 2011 Shaun Jackman <sjackman at debian.org>
License: ISC
Permission to use, copy, modify, and/or distribute this software for any
purpose with or without fee is hereby granted, provided that the above
diff --git a/debian/gmap.1 b/debian/gmap.1
index aa488f0..6a89b8e 100644
--- a/debian/gmap.1
+++ b/debian/gmap.1
@@ -1,4 +1,4 @@
-.TH GMAP "1" "Mar 2011" "GMAP 2011-03-11" "User Commands"
+.TH GMAP "1" "August 2011" "GMAP 2011-08-15" "User Commands"
.SH NAME
gmap \- Genomic Mapping and Alignment Program
.SH SYNOPSIS
@@ -18,6 +18,11 @@ Genome directory
Genome database. If argument is '?' (with
the quotes), this command lists available databases.
.TP
+\fB-k\fR, \fB--kmer\fR=\fIINT\fR
+kmer size to use in genome database (allowed values: 12-15). If not
+specified, the program will find the highest available kmer size in
+the genome database
+.TP
\fB\-G\fR, \fB\-\-genomefull\fR
Use full genome (all ASCII chars allowed;
built explicitly during setup), not
@@ -44,28 +49,32 @@ Computation options
2 allocate mmap & preload mmap & preload (default)
3 allocate allocate mmap & preload
4 allocate allocate allocate
+ 5 expand allocate allocate
Note: For a single sequence, all data structures use mmap.
-If mmap not available and allocate not chosen, then will use fileio (slow)
+If mmap not available and allocate not chosen, then will use fileio
+(very slow)
+.TP
+\fB-K\fR, \fB--intronlength\fR=\fIINT\fR
+Max length for one internal intron (default 1000000)
.TP
-\fB\-K\fR, \fB\-\-intronlength\fR=\fIINT\fR
-Max length for one intron (default 1000000)
+\fB-w\fR, \fB--localsplicedist\fR=\fIINT\fR
+Max length for known splice sites at ends of sequence (default 200000)
.TP
\fB\-L\fR, \fB\-\-totallength\fR=\fIINT\fR
Max total intron length (default 2400000)
.TP
\fB\-x\fR, \fB\-\-chimera-margin\fR=\fIINT\fR
Amount of unaligned sequence that triggers
-search for a chimera (default off)
+search for the remaining sequence (default 40).
+Enables alignment of chimeric reads, and may help
+with some non-chimeric reads. To turn off, set to 0.
.TP
\fB\-t\fR, \fB\-\-nthreads\fR=\fIINT\fR
Number of worker threads
.TP
-\fB\-s\fR, \fB\-\-altstrain\fR
-Search alternate strains in addition
-.TP
\fB\-C\fR, \fB\-\-chrsubsetfile\fR=\fIfilename\fR
-User\-suppled chromosome subset file
+User\-supplied chromosome subset file
.TP
\fB\-c\fR, \fB\-\-chrsubset\fR=\fIstring\fR
Chromosome subset to search
@@ -78,11 +87,19 @@ sense_filter, antisense_filter, or auto (default))
Trim end exons with fewer than given number of matches
(in nt, default 12)
.TP
-\fB\-X\fR, \fB\-\-canonical\fR=\fIINT\fR
-Reward for canonical and semi\-canonical introns
+\fB--cross-species\fR
+For cross-species alignments, use a more sensitive search for
+canonical splicing
+.TP
+\fB--canonical-mode\fR=\fIINT\fR
+Reward for canonical and semi-canonical introns
0=low reward, 1=high reward (default), 2=low reward for
high\-identity sequences and high reward otherwise
.TP
+\fB--allow-close-indels\fR=\fIINT\fR
+Allow an insertion and deletion close to each other
+(0=no, 1=yes (default), 2=only for high-quality alignments)
+.TP
\fB\-p\fR, \fB\-\-prunelevel\fR
Pruning level: 0=no pruning (default), 1=poor seqs,
2=repetitive seqs, 3=poor and repetitive
@@ -114,15 +131,17 @@ Print protein sequence (cDNA)
Print protein sequence (genomic)
.TP
\fB\-f\fR, \fB\-\-format\fR=\fIINT\fR
-Format for output
- 1 or psl = PSL (BLAT) format,
- 2 or gff3_gene = GFF3 gene format,
- 3 or gff3_match_cdna = GFF3 cDNA_match format,
- 4 or gff3_match_est = GFF3 EST_match format,
- 6 or splicesites = splicesites output (for GSNAP),
- 7 or map_exons = IIT FASTA exon map format,
- 8 or map_genes = IIT FASTA map format,
- 9 or coords = coords in table format,
+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,
+ gff3_match_cdna (or 3)= GFF3 cDNA_match format,
+ gff3_match_est (or 4) = GFF3 EST_match format,
+ splicesites (or 6) = splicesites output (for GSNAP splicing file),
+ introns = introns output (for GSNAP splicing file),
+ map_exons (or 7) = IIT FASTA exon map format,
+ map_genes (or 8) = IIT FASTA map format,
+ coords (or 9) = coords in table format,
sampe = SAM format (setting paired_read bit in flag),
samse = SAM format (without setting paired_read bit)
.SS
@@ -132,6 +151,10 @@ Output options
Maximum number of paths to show. If set to 0,
prints two paths if chimera detected, else one.
.TP
+\fB--quiet-if-excessive\fR
+If more than maximum number of paths are found, then nothing is
+printed.
+.TP
\fB\-O\fR, \fB\-\-ordered\fR
Print output in same order as input (relevant
only if there is more than one worker thread)
@@ -160,6 +183,11 @@ previously using snpindex) for reporting output
Basename for multiple-file output, separately for nomapping,
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
+number of results to be printed exceeds this size, the worker threads
+are halted until the backlog is cleared
+.TP
\fB\-F\fR, \fB\-\-fulllength\fR
Assume full\-length protein, starting with Met
.TP
@@ -187,6 +215,28 @@ Value to put into read-group id (RG-ID) field
.TP
\fB\-\-read\-group\-name\fR=\fISTRING\fR
Value to put into read-group name (RG-SM) field
+.TP
+\fB--read-group-library\fR=\fISTRING\fR
+Value to put into read-group library (RG-LB) field
+.TP
+\fB--read-group-platform\fR=\fISTRING\fR
+Value to put into read-group library (RG-PL) field
+.SS
+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)
+
+Default is sanger (no quality print shift)
+SAM output files should have quality scores in sanger protocol.
+Or you can specify the print shift with this flag:
+.TP
+\fB-j\fR, \fB--quality-print-shift\fR=\fIINT\fR
+Shift FASTQ quality scores by this amount in output
+(default is 0 for sanger protocol; to change Illumina input to Sanger
+output, select -31)
.SS
External map file options
.TP
diff --git a/debian/gsnap.1 b/debian/gsnap.1
index bc725a3..12ebb94 100644
--- a/debian/gsnap.1
+++ b/debian/gsnap.1
@@ -1,4 +1,4 @@
-.TH GSNAP "1" "Mar 2011" "GMAP 2011-03-11" "User Commands"
+.TH GSNAP "1" "August 2011" "GMAP 2011-08-15" "User Commands"
.SH NAME
gsnap \- Genomic Short-read Nucleotide Alignment Program
.SH SYNOPSIS
@@ -17,6 +17,11 @@ Genome directory
\fB\-d\fR, \fB\-\-db\fR=\fISTRING\fR
Genome database
.TP
+\fB-k\fR, \fB--kmer\fR=\fIINT\fR
+kmer size to use in genome database (allowed values: 12-15). If not
+specified, the program will find the highest available kmer size in
+the genome database
+.TP
\fB\-q\fR, \fB\-\-part\fR=\fIINT/INT\fR
Process only the i\-th out of every n sequences
e.g., 0/100 or 99/100 (useful for distributing jobs to a computer farm).
@@ -28,9 +33,6 @@ at a time for efficiency) (default 1000)
\fB\-\-barcode\-length\fR=\fIINT\fR
Amount of barcode to remove from start of read (default 0)
.TP
-\fB\-\-pc\-linefeeds\fR
-Strip PC line feeds (ASCII 13) from input
-.TP
\fB\-o\fR, \fB\-\-orientation=\fISTRING\fR
Orientation of paired-end reads
Allowed values: FR (fwd-rev, or typical Illumina; default),
@@ -39,7 +41,7 @@ FR (rev-fwd, for circularized inserts), or FF (fwd-fwd, same strand)
Computation options
.PP
Note: GSNAP has an ultrafast algorithm for calculating mismatches up to and including
-((readlength+2)/12 \- 2) ("ultrafast mismatches"). The program will run fastest if
+((readlength+2)/kmer \- 2) ("ultrafast mismatches"). The program will run fastest if
max\-mismatches (plus suboptimal\-levels) is within that value.
Also, indels, especially end indels, take longer to compute, although the algorithm
is still designed to be fast.
@@ -51,31 +53,37 @@ is still designed to be fast.
2 allocate mmap & preload mmap & preload (default)
3 allocate allocate mmap & preload
4 allocate allocate allocate
+ 5 expand allocate allocate
Note: For a single sequence, all data structures use mmap.
-If mmap not available and allocate not chosen, then will use fileio (slow)
+If mmap not available and allocate not chosen, then will use fileio
+(very slow)
.TP
\fB\-m\fR, \fB\-\-max\-mismatches\fR=\fIFLOAT\fR
Maximum number of mismatches allowed (if not specified, then
-defaults to the ultrafast level of ((readlength+2)/12 \- 2))
+defaults to the ultrafast level of ((readlength+2)/kmer \- 2))
If specified between 0.0 and 1.0, then treated as a fraction
of each read length. Otherwise, treated as an integral number
of mismatches (including indel and splicing penalties)
For RNA-Seq, you may need to increase this value slightly
to align reads extending past the ends of an exon.
.TP
-\fB\-\-terminal\-penalty\fR=\fIINT\fR
-Penalty for a terminal alignment (alignment from one end of the read
-to the best possible position at the other end) (default 1)
+\fB--query-unk-mismatch\fR=\fIINT\fR
+Whether to count unknown (N) characters in the query as a mismatch
+(0=no (default), 1=yes)
+.TP
+\fB--genome-unk-mismatch\fR=\fIINT\fR
+Whether to count unknown (N) characters in the genome as a mismatch
+(0=no, 1=yes (default))
.TP
\fB\-i\fR, \fB\-\-indel\-penalty\fR=\fIINT\fR
-Penalty for an indel (default 1).
+Penalty for an indel (default 2).
Counts against mismatches allowed. To find indels, make
-indel\-penalty less than or equal to max\-mismatches
-For 2\-base reads, need to set indel\-penalty somewhat high
+indel-penalty less than or equal to max-mismatches.
+A value < 2 can lead to false positives at read ends
.TP
-\fB\-I\fR, \fB\-\-indel\-endlength\fR=\fIINT\fR
-Minimum length at end required for indel alignments (default 3)
+\fB\-\-indel\-endlength\fR=\fIINT\fR
+Minimum length at end required for indel alignments (default 4)
.TP
\fB\-y\fR, \fB\-\-max\-middle\-insertions\fR=\fIINT\fR
Maximum number of middle insertions allowed (default 9)
@@ -103,7 +111,11 @@ on non\-unique or repetitive reads
4 = greedy repetitive: mask frequent and repetitive oligomers first, then try no masking if alignments not found
.TP
\fB-a\fR, \fB--adapter-strip\fR=\fISTRING\fR
-Method for removing adapters from reads. Currently allowed values: paired
+Method for removing adapters from reads. Currently allowed values:
+off, paired.
+Default is "paired", which removes adapters from paired-end reads if a
+concordant or paired alignment cannot be found from the original read.
+To turn off, use the value "off".
.TP
\fB\-\-trim\-mismatch\-score\fR=\fIINT\fR
Score to use for mismatches when trimming at ends (default is -3;
@@ -117,37 +129,94 @@ location of genome index files specified using -D and -d)
Use database containing known SNPs (in <STRING>.iit, built
previously using snpindex) for tolerance to SNPs
.TP
-\fB\-C\fR, \fB\-\-cmetdir\fR=\fISTRING\fR
+\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)
.TP
-\fB\-c\fR, \fB\-\-cmet\fR
-Use database for methylcytosine experiments, built
-previously using cmetindex)
+\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)
+.TP
+\fB--mode\fR=\fISTRING\fR
+Alignment mode: standard (default), cmet, or atoi
+.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)
+.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)
+.TP
+\fB--use-runlength\fR=\fISTRING\fR
+Use this runlength IIT file to resolve concordant multiple results
.TP
\fB\-t\fR, \fB\-\-nthreads\fR=\fIINT\fR
Number of worker threads
.SS
+Options for GMAP alignment within GSNAP
+.TP
+\fB--gmap-mode\fR=\fISTRING\fR
+Cases to use GMAP for complex alignments containing multiple splices
+or indels.
+Allowed values: none, pairsearch, terminal, improve (or multiple,
+separated by commas). Default: pairsearch,terminal,improve
+.TP
+\fB--trigger-score-for-gmap\fR=\fIINT\fR
+Try GMAP pairsearch on nearby genomic regions if best score (the total
+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 3). 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 3). Requires terminal in --gmap-mode
+.TP
+\fB--max-gmap-improvement\fR=\fIINT\fR
+Perform GMAP improvement on nearby genomic regions up to this many
+.SS
+Genes options for RNA-Seq
+.TP
+\fB-g, --genes\fR=\fISTRING\fR
+Look for known genes in <STRING>.iit, to be used for resolving
+multiple mapping reads. See README instructions for the correct
+formatting of a genes IIT file.
+.TP
+\fB--favor-multiexon\fR
+In resolving multiple mapping reads, overlaps with known
+multi-exon genes are favored over those with known single-exon
+genes. This favors spliced genes over psuedogenes.
+.SS
Splicing options for RNA\-Seq
.TP
-\fB\-s\fR, \fB\-\-splicesites\fR=\fISTRING\fR
-Look for splicing involving known splice sites
-(in <STRING>.iit), at short or long distances
.TP
-\fB\-S\fR, \fB\-\-splicetrie\-precompute\fR=\fIINT\fR
-Pre-compute splicetrie for all known splice sites
-(0=no, 1=yes (default)). Requires --splicesites flag
-and multiple sequence input.
+\fB-N,\fR \fB--novelsplicing\fR=\fIINT\fR
+Look for novel splicing (0=no (default), 1=yes)
+.TP
+\fB-S\fR, \fB--splicesdir\fR=\fISTRING\fR
+Directory for splicing involving known sites or known introns,
+as specified by the -s or --use-splices flag (default is
+directory computed from -D and -d flags)
.TP
-\fB\-N\fR, \fB\-\-novelsplicing\fR=\fIINT\fR
-Look for novel splicing, not in known splice sites (if \fB\-s\fR provided)
+\fB\-s\fR, \fB--use-splices\fR=\fISTRING\fR
+Look for splicing involving known sites or known introns
+(in <STRING>.iit), at short or long distances.
+See README instructions for the distinction between known sites and
+known introns
.TP
\fB\-\-novel\-doublesplices\fR
Allow GSNAP to look for two splices in a single-end involving novel
splice sites (default is not to allow this). Caution: this option
can slow down the program considerably. A better way to detect
-double splices is with known splice sites, using the
-\fB\-\-splicesites\fR option.
+double splices is with known splice sites, using the --use-splices
+option.
.TP
\fB-w\fR, \fB\-\-localsplicedist\fR=\fIINT\fR
Definition of local novel splicing event (default 200000)
@@ -163,9 +232,6 @@ Counts against mismatches allowed
Penalty for a distant splice (default 3).
Counts against mismatches allowed
.TP
-\fB\-k\fR, \fB\-\-local\-splice\-endlength\fR=\fIINT\fR
-Minimum length at end required for local spliced alignments (default 15, min is 14)
-.TP
\fB\-K\fR, \fB\-\-distant\-splice\-endlength\fR=\fIINT\fR
Minimum length at end required for distant spliced alignments (default 16, min is 14)
.TP
@@ -174,6 +240,12 @@ Minimum length at end required for short-end spliced alignments (default 2)
.TP
\fB\-\-distant\-splice\-identity\fR=\fIFLOAT\fR
Minimum identity at end required for distant spliced alignments (default 0.95)
+.TP
+\fB--antistranded-penalty\fR=\fIINT\fR
+Penalty for antistranded splicing when using stranded RNA-Seq
+protocols. A positive value, such as 1, expects antisense on the
+first read and sense on the second read. Default is 0, which treats
+sense and antisense equally well
.SS
Options for paired\-end reads
.TP
@@ -185,18 +257,11 @@ Max total genomic length for paired reads
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.
-.TP
-\fB\-\-pairexpect\fR=\fIINT\fR
-Expected paired-end length (default 200)
-.TP
-\fB\-\-pairdev\fR=\fIINT\fR
-Allowable deviation from expected paired-end length, used for
-discriminating between alternative alignments (default 50)
.SS
Options for quality scores
.TP
\fB\-\-quality\-protocol\fR=\fISTRING\fR
-Protocol for input quality scores. Allowed values:
+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)
@@ -214,6 +279,11 @@ FASTQ quality scores are zero at this ASCII value
Shift FASTQ quality scores by this amount in output
(default is 0 for sanger protocol; to change Illumina input
to Sanger output, select -31)
+.TP
+\fB--mapq-unique-score\fR=\fIINT\fR
+For multiple results, consider as a unique result if only one of the
+results has a MAPQ score equal or greater than this (if not selected,
+then reports all multiple results, up to npaths)
.SS
Output options
.TP
@@ -233,6 +303,10 @@ For GSNAP output in SNP-tolerant alignment, shows all differences
relative to the reference genome as lower case (otherwise, it shows
all differences relative to both the reference and alternate genome)
.TP
+\fB--clip-overlap\fR
+For paired-end reads whose alignments overlap, clip the overlapping
+region.
+.TP
\fB\-\-print\-snps\fR
Print detailed information about SNPs in reads (works only if \fB\-v\fR also selected)
(not fully implemented yet)
@@ -252,6 +326,11 @@ Another format type, other than default.
Currently implemented: sam
Also allowed, but not installed at compile-time: goby
(To install, need to re-compile with appropriate options)
+.TP
+\fB--output-buffer-size\fR=\fIINT\fR
+Buffer size, in queries, for output thread (default 1000). When the
+number of results to be printed exceeds this size, the worker threads
+are halted until the backlog is cleared
.SS
Options for SAM output
.TP
@@ -266,6 +345,12 @@ Value to put into read-group id (RG-ID) field
.TP
\fB\-\-read\-group\-name\fR=\fISTRING\fR
Value to put into read-group name (RG-SM) field
+.TP
+\fB--read-group-library\fR=\fISTRING\fR
+Value to put into read-group library (RG-LB) field
+.TP
+\fB--read-group-platform\fR=\fISTRING\fR
+Value to put into read-group library (RG-PL) field
.SS
Help options
.TP
diff --git a/debian/install b/debian/install
index 30ee3d2..8dc8108 100644
--- a/debian/install
+++ b/debian/install
@@ -1,18 +1,24 @@
usr/bin/gmap
usr/bin/gsnap
usr/bin/gmap_setup
+usr/bin/atoiindex /usr/lib/gmap
usr/bin/cmetindex /usr/lib/gmap
-usr/bin/dibaseindex /usr/lib/gmap
+usr/bin/dbsnp_iit /usr/lib/gmap
usr/bin/fa_coords /usr/lib/gmap
usr/bin/get-genome /usr/lib/gmap
+usr/bin/gmap_build /usr/lib/gmap
usr/bin/gmap_compress /usr/lib/gmap
usr/bin/gmap_process /usr/lib/gmap
usr/bin/gmap_reassemble /usr/lib/gmap
usr/bin/gmap_uncompress /usr/lib/gmap
usr/bin/gmapindex /usr/lib/gmap
usr/bin/gsnap_tally /usr/lib/gmap
+usr/bin/gtf_genes /usr/lib/gmap
+usr/bin/gtf_splicesites /usr/lib/gmap
usr/bin/iit_dump /usr/lib/gmap
usr/bin/iit_get /usr/lib/gmap
usr/bin/iit_store /usr/lib/gmap
usr/bin/md_coords /usr/lib/gmap
+usr/bin/psl_genes /usr/lib/gmap
+usr/bin/psl_splicesites /usr/lib/gmap
usr/bin/snpindex /usr/lib/gmap
diff --git a/debian/patches/install-data-local b/debian/patches/install-data-local
index 56ee76a..41659e1 100644
--- a/debian/patches/install-data-local
+++ b/debian/patches/install-data-local
@@ -2,7 +2,7 @@ Description: Add DESTDIR to install-data-local
--- gmap.orig/Makefile.in
+++ gmap/Makefile.in
-@@ -650,7 +650,7 @@
+@@ -651,7 +651,7 @@
install-data-local:
--
Align mRNA and EST sequences to a genome
More information about the debian-med-commit
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