The following commit has been merged in the master branch: commit fa026f0479f1ce52255c6f25dba299b7de54d5f6 Author: Shaun Jackman <sjack...@debian.org> Date: Wed Dec 7 13:21:47 2011 -0800
New upstream release. diff --git a/debian/changelog b/debian/changelog index 758ddfb..3809c40 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +gmap (2011-11-30-1) unstable; urgency=low + + * New upstream release. + + -- Shaun Jackman <sjack...@debian.org> Wed, 07 Dec 2011 10:46:12 -0800 + gmap (2011-10-16-1) unstable; urgency=low * New upstream release. diff --git a/debian/gmap.1 b/debian/gmap.1 index 6958409..37a581a 100644 --- a/debian/gmap.1 +++ b/debian/gmap.1 @@ -1,4 +1,4 @@ -.TH GMAP "1" "August 2011" "GMAP 2011-08-15" "User Commands" +.TH GMAP "1" "Nov 2011" "GMAP 2011-11-30" "User Commands" .SH NAME gmap \- Genomic Mapping and Alignment Program .SH SYNOPSIS @@ -84,7 +84,8 @@ Max total intron length (default 2400000) Amount of unaligned sequence that triggers 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. +with some non-chimeric reads. To turn off, set to +a large value (greater than the query length). .TP \fB\-t\fR, \fB\-\-nthreads\fR=\fIINT\fR Number of worker threads @@ -175,6 +176,11 @@ prints two paths if chimera detected, else one. If more than maximum number of paths are found, then nothing is printed. .TP +\fB--suboptimal-score\fR=\fIINT\fR +Report only paths whose score is within this value of the +best path. By default, if this option is not provided, +the program prints all paths found. +.TP \fB\-O\fR, \fB\-\-ordered\fR Print output in same order as input (relevant only if there is more than one worker thread) @@ -226,10 +232,6 @@ Options for SAM output \fB\-\-no\-sam\-headers\fR Do not print headers beginning with '@' .TP -\fB\-\-noncanonical\-splices\fR=\fISTRING\fR -Print non-canonical genomic gaps greater than 20 nt -in CIGAR string as STRING. Allowed values: N (default), D. -.TP \fB\-\-read\-group\-id\fR=\fISTRING\fR Value to put into read-group id (RG-ID) field .TP diff --git a/debian/gmap_setup.1 b/debian/gmap_setup.1 index 8338d17..aab9a93 100644 --- a/debian/gmap_setup.1 +++ b/debian/gmap_setup.1 @@ -1,4 +1,4 @@ -.TH GMAP_SETUP "1" "Aug 2010" "GMAP 2010-07-27" "User Commands" +.TH GMAP_SETUP "1" "Nov 2011" "GMAP 2011-11-30" "User Commands" .SH NAME gmap_setup \- create a genome database for GMAP or GSNAP .SH SYNOPSIS diff --git a/debian/gsnap.1 b/debian/gsnap.1 index a70434b..ca9500b 100644 --- a/debian/gsnap.1 +++ b/debian/gsnap.1 @@ -1,4 +1,4 @@ -.TH GSNAP "1" "August 2011" "GMAP 2011-08-15" "User Commands" +.TH GSNAP "1" "Nov 2011" "GMAP 2011-11-30" "User Commands" .SH NAME gsnap \- Genomic Short-read Nucleotide Alignment Program .SH SYNOPSIS @@ -104,8 +104,14 @@ Whether to count unknown (N) characters in the genome as a mismatch .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. +read to the best possible position at the other end) (default 2). +For example, if this value is 2, then if GSNAP finds an exact or +1-mismatch alignment, it will not try to find a terminal alignment. +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. .TP \fB\-i\fR, \fB\-\-indel\-penalty\fR=\fIINT\fR Penalty for an indel (default 2). @@ -141,7 +147,13 @@ 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; -to turn off trimming, specify 0) +to turn off trimming, specify 0). Warning: turning trimming off +will give false positive mismatches at the ends of reads +.TP +\fB--trim-indel-score\fR=\fIINT\fR +Score to use for indels when trimming at ends (default is -4; +to turn off trimming, specify 0). Warning: turning trimming off +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 @@ -230,6 +242,12 @@ Look for splicing involving known sites or known introns See README instructions for the distinction between known sites and known introns .TP +\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 +.TP \fB\-w\fR, \fB\-\-localsplicedist\fR=\fIINT\fR Definition of local novel splicing event (default 200000) .TP @@ -259,6 +277,11 @@ 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 +.TP +\fB--merge-distant-samechr\fR +Report distant splices on the same chromosome as a single splice, if possible. +Will produce a single SAM line instead of two SAM lines, which is also done +for translocations, inversions, and scramble events .SS Options for paired\-end reads .TP @@ -270,6 +293,14 @@ without splicing (default 1000). Used if -N or -s is not specified. 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, used for calling splices in medial part of +paired-end reads (default 200) +.TP +\fB--pairdev\fR=\fIINT\fR +Allowable deviation from expected paired-end length, used for +calling splices in medial part of paired-end reads (default 25) .SS Options for quality scores .TP @@ -292,11 +323,6 @@ 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 -- 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