[med-svn] [SCM] gmap branch, master, updated. upstream/2011-08-15-23-gce80089

Shaun Jackman sjackman at debian.org
Thu Sep 15 00:45:15 UTC 2011 

The following commit has been merged in the master branch:
commit ce800895fb3da208229f877b5e8025fd72d80ae2
Author: Shaun Jackman <sjackman at debian.org>
Date:   Wed Sep 14 17:44:09 2011 -0700

    New upstream release.

diff --git a/debian/changelog b/debian/changelog
index c3c12ac..e8cfaf8 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+gmap (2011-09-09-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Shaun Jackman <sjackman at debian.org>  Wed, 14 Sep 2011 17:09:21 -0700
+
 gmap (2011-08-15-1) unstable; urgency=low
 
   * New upstream release.
diff --git a/debian/gmap.1 b/debian/gmap.1
index 6a89b8e..dc1d6a8 100644
--- a/debian/gmap.1
+++ b/debian/gmap.1
@@ -29,7 +29,15 @@ built explicitly during setup), not
 compressed version
 .TP
 \fB\-g\fR, \fB\-\-gseg\fR=\fIfilename\fR
-User\-suppled genomic segment
+User-supplied genomic segment
+.TP
+\fB-2\fR, \fB--pairalign\fR
+Align two sequences in FASTA format via stdin, first one being
+genomic and second one being cDNA
+.TP
+\fB--cmdline\fR=\fISTRING\fR,\fISTRING\fR
+Align these two sequences provided on the command line,
+first one being genomic and second one being cDNA
 .TP
 \fB\-q\fR, \fB\-\-part\fR=\fIINT\fR/\fIINT\fR
 Process only the i-th out of every n sequences
@@ -55,6 +63,10 @@ Note: For a single sequence, all data structures use mmap.
 If mmap not available and allocate not chosen, then will use fileio
 (very slow)
 .TP
+\fB--nosplicing\fR
+Turns off splicing (useful for aligning genomic sequences
+onto a genome)
+.TP
 \fB-K\fR, \fB--intronlength\fR=\fIINT\fR
 Max length for one internal intron (default 1000000)
 .TP
@@ -100,6 +112,10 @@ high\-identity sequences and high reward otherwise
 Allow an insertion and deletion close to each other
 (0=no, 1=yes (default), 2=only for high-quality alignments)
 .TP
+\fB--microexon-spliceprob\fR=\fIFLOAT\fR
+Allow microexons only if one of the splice site probabilities is
+greater than this value (default 0.90)
+.TP
 \fB\-p\fR, \fB\-\-prunelevel\fR
 Pruning level: 0=no pruning (default), 1=poor seqs,
 2=repetitive seqs, 3=poor and repetitive
diff --git a/debian/gsnap.1 b/debian/gsnap.1
index 12ebb94..0578686 100644
--- a/debian/gsnap.1
+++ b/debian/gsnap.1
@@ -37,6 +37,21 @@ Amount of barcode to remove from start of read (default 0)
 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)
+.TP
+\fB--fastq-id-start\fR=\fIINT\fR
+Starting position of identifier in FASTQ header, space-delimited (>= 1)
+.TP
+\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)
+ @SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
+  start=1, end=1
+   => identifier is SRR001666.1
+  start=2, end=2
+   => 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
 .SS
 Computation options
 .PP
@@ -76,6 +91,11 @@ Whether to count unknown (N) characters in the query as a mismatch
 Whether to count unknown (N) characters in the genome as a mismatch
 (0=no, 1=yes (default))
 .TP
+\fB--terminal-threshold\fR=\fIINT\fR
+Threshold for searching for a terminal alignment (from one end of the
+read to the best possible position at the other end) (default 3).
+To turn off terminal alignments, set this to a high value.
+.TP
 \fB\-i\fR, \fB\-\-indel\-penalty\fR=\fIINT\fR
 Penalty for an indel (default 2).
 Counts against mismatches allowed. To find indels, make
@@ -101,15 +121,6 @@ Maximum number of end deletions allowed (default 6)
 Report suboptimal hits beyond best hit (default 0)
 All hits with best score plus suboptimal-levels are reported
 .TP
-\fB\-R\fR, \fB\-\-masking\fR=\fIINT\fR
-Masking of frequent/repetitive oligomers to avoid spending time
-on non\-unique or repetitive reads
- 0 = no masking (will try to find non\-unique or repetitive matches)
- 1 = mask frequent oligomers
- 2 = mask frequent and repetitive oligomers (fastest) (default)
- 3 = greedy frequent: mask frequent oligomers first, then try no masking if alignments not found
- 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:
 off, paired.
@@ -143,7 +154,8 @@ 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)
+(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
@@ -151,7 +163,8 @@ Use this tally IIT file to resolve concordant multiple results
 \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)
+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
@@ -181,6 +194,10 @@ 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
+.TP
+\fB--microexon-spliceprob\fR=\fIFLOAT\fR
+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
@@ -203,7 +220,8 @@ Look for novel splicing (0=no (default), 1=yes)
 \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)
+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
 Look for splicing involving known sites or known introns

-- 
Align mRNA and EST sequences to a genome

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