[med-svn] [SCM] gmap branch, master, updated. upstream/2011-09-14-27-gf9ff31c

Shaun Jackman sjackman at debian.org
Wed Oct 19 23:59:05 UTC 2011 

The following commit has been merged in the master branch:
commit f9ff31c8c859f6aeee6045ae86eda7bf4b98b865
Author: Shaun Jackman <sjackman at debian.org>
Date:   Wed Oct 19 16:57:17 2011 -0700

    New upstream release.

diff --git a/debian/changelog b/debian/changelog
index c348c40..758ddfb 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+gmap (2011-10-16-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Shaun Jackman <sjackman at debian.org>  Wed, 19 Oct 2011 15:40:36 -0700
+
 gmap (2011-09-14-1) unstable; urgency=low
 
   * New upstream release.
diff --git a/debian/gmap.1 b/debian/gmap.1
index dc1d6a8..6958409 100644
--- a/debian/gmap.1
+++ b/debian/gmap.1
@@ -67,6 +67,10 @@ If mmap not available and allocate not chosen, then will use fileio
 Turns off splicing (useful for aligning genomic sequences
 onto a genome)
 .TP
+\fB--min-intronlength\fR=\fIINT\fR
+Min length for one internal intron (default 9).  Below this size,
+a genomic gap will be considered a deletion rather than an intron.
+.TP
 \fB-K\fR, \fB--intronlength\fR=\fIINT\fR
 Max length for one internal intron (default 1000000)
 .TP
diff --git a/debian/gsnap.1 b/debian/gsnap.1
index 0578686..a70434b 100644
--- a/debian/gsnap.1
+++ b/debian/gsnap.1
@@ -36,7 +36,7 @@ Amount of barcode to remove from start of read (default 0)
 \fB\-o\fR, \fB\-\-orientation=\fISTRING\fR
 Orientation of paired-end reads
 Allowed values: FR (fwd-rev, or typical Illumina; default),
-FR (rev-fwd, for circularized inserts), or FF (fwd-fwd, same strand)
+RF (rev-fwd, for circularized inserts), or FF (fwd-fwd, same strand)
 .TP
 \fB--fastq-id-start\fR=\fIINT\fR
 Starting position of identifier in FASTQ header, space-delimited (>= 1)
@@ -44,7 +44,9 @@ Starting position of identifier in FASTQ header, space-delimited (>= 1)
 \fB--fastq-id-end\fR=\fIINT\fR
 Ending position of identifier in FASTQ header, space-delimited (>= 1)
  Examples:
- @HWUSI-EAS100R:6:73:941:1973#0/1 start=1, end=1 (default)
+ @HWUSI-EAS100R:6:73:941:1973#0/1
+  start=1, end=1 (default)
+   => identifier is HWUSI-EAS100R:6:73:941:1973#0
  @SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
   start=1, end=1
    => identifier is SRR001666.1
@@ -52,6 +54,15 @@ Ending position of identifier in FASTQ header, space-delimited (>= 1)
    => identifier is 071112_SLXA-EAS1_s_7:5:1:817:345
   start=1, end=2
    => identifier is SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345
+.TP
+\fB--filter-chastity\fR=\fISTRING\fR
+Skips reads marked by the Illumina chastity program.  Expecting a string
+after the accession having a 'Y' after the first colon, like this:
+ @accession 1:Y:0:CTTGTA
+where the 'Y' signifies filtering by chastity.
+Values: off (default), either, both.  For 'either', a 'Y' on either end
+of a paired-end read will be filtered.  For 'both', a 'Y' is required
+on both ends of a paired-end read (or on the only end of a single-end read).
 .SS
 Computation options
 .PP
@@ -150,7 +161,9 @@ Directory for A-to-I RNA editing index files (created using atoiindex)
 -d)
 .TP
 \fB--mode\fR=\fISTRING\fR
-Alignment mode: standard (default), cmet, or atoi
+Alignment mode: standard (default), cmet-stranded, cmet-nonstranded,
+atoi-stranded, or atoi-nonstranded. Non-standard modes requires you
+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
@@ -199,62 +212,44 @@ Perform GMAP improvement on nearby genomic regions up to this many
 Allow microexons only if one of the splice site probabilities is
 greater than this value (default 0.90)
 .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
 .TP
 \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
+\fB--splicingdir\fR=\fISTRING\fR
 Directory for splicing involving known sites or known introns,
-as specified by the -s or --use-splices flag (default is
+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-splices\fR=\fISTRING\fR
+\fB\-s\fR, \fB--use-splicing\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 --use-splices
-option.
-.TP
-\fB-w\fR, \fB\-\-localsplicedist\fR=\fIINT\fR
-Definition of local novel splicing event (default 200000)
-.TP
 \fB\-w\fR, \fB\-\-localsplicedist\fR=\fIINT\fR
 Definition of local novel splicing event (default 200000)
 .TP
 \fB\-e\fR, \fB\-\-local\-splice\-penalty\fR=\fIINT\fR
-Penalty for a local splice (default 0).
-Counts against mismatches allowed
+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 3).
+Penalty for a distant splice (default 3). A distant splice is one where
+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
 \fB\-K\fR, \fB\-\-distant\-splice\-endlength\fR=\fIINT\fR
-Minimum length at end required for distant spliced alignments (default 16, min is 14)
+Minimum length at end required for distant spliced alignments (default 16, min
+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
 .TP
 \fB\-\-distant\-splice\-identity\fR=\fIFLOAT\fR
 Minimum identity at end required for distant spliced alignments (default 0.95)
@@ -268,8 +263,8 @@ sense and antisense equally well
 Options for paired\-end reads
 .TP
 \fB\-\-pairmax-dna\fR=\fIINT\fR
-Max total genomic length for paired reads
-(default 1000). Should increase for RNA-Seq reads.
+Max total genomic length for DNA-Seq paired reads, or other reads
+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
diff --git a/debian/patches/install-data-local b/debian/patches/install-data-local
index 41659e1..e09331b 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
-@@ -651,7 +651,7 @@
+@@ -653,7 +653,7 @@
  
  
  install-data-local:

-- 
Align mRNA and EST sequences to a genome

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