The following commit has been merged in the master branch: commit ce800895fb3da208229f877b5e8025fd72d80ae2 Author: Shaun Jackman <sjack...@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 <sjack...@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 _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit