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commit 09015de408e84888f68370f581b271103e95bb1e Author: Alexandre Mestiashvili <[email protected]> Date: Thu Mar 12 18:03:22 2015 +0100 d/*.1: updated man pages --- debian/gmap.1 | 56 ++++++++++++++++++++++-------------- debian/gmap_build.1 | 22 +++++++++----- debian/gsnap.1 | 83 +++++++++++++++++++++++++++++++---------------------- 3 files changed, 97 insertions(+), 64 deletions(-) diff --git a/debian/gmap.1 b/debian/gmap.1 index 2537905..cfb1f91 100644 --- a/debian/gmap.1 +++ b/debian/gmap.1 @@ -1,4 +1,4 @@ -.TH GMAP "1" "GMAP 2014-10-22" "User Commands" +.TH GMAP "1" "GMAP 2014-12-23" "User Commands" .SH NAME gmap \- Genomic Mapping and Alignment Program .SH SYNOPSIS @@ -11,7 +11,8 @@ Align the sequences QUERY to the reference, specified with .SS Input options (must include \fB\-d\fR or \fB\-g\fR) .TP \fB\-D\fR, \fB\-\-dir\fR=\fI\,directory\/\fR -Genome directory +Genome directory. Default (as specified by \fB\-\-with\-gmapdb\fR to the configure program) is +\fI\,/var/cache/gmap\/\fP .TP \fB\-d\fR, \fB\-\-db\fR=\fI\,STRING\/\fR Genome database. If argument is '?' (with @@ -72,8 +73,8 @@ Batch mode (default = 2) 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 -Note about \fB\-\-batch\fR and offsets: Expansion of offsets can be controlled independently by the \fB\-\-expand\-offsets\fR flag. -The \fB\-\-batch\fR=\fI\,5\/\fR option is equivalent +Note about \fB\-\-batch\fR and offsets: Expansion of offsets can be controlled +independently by the \fB\-\-expand\-offsets\fR flag. The \fB\-\-batch\fR=\fI\,5\/\fR option is equivalent to \fB\-\-batch\fR=\fI\,4\/\fR plus \fB\-\-expand\-offsets\fR=\fI\,1\/\fR .TP \fB\-\-expand\-offsets\fR=\fI\,INT\/\fR @@ -90,11 +91,11 @@ 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=\fI\,INT\/\fR -Max length for one internal intron (default 1000000) +Max length for one internal intron (default 200000) .TP \fB\-w\fR, \fB\-\-localsplicedist\fR=\fI\,INT\/\fR Max length for known splice sites at ends of sequence -(default 2,000,000) +(default 2000000) .TP \fB\-L\fR, \fB\-\-totallength\fR=\fI\,INT\/\fR Max total intron length (default 2400000) @@ -121,7 +122,7 @@ sense_filter, antisense_filter,or auto (default)) .TP \fB\-H\fR, \fB\-\-trimendexons\fR=\fI\,INT\/\fR Trim end exons with fewer than given number of matches -(in nt, default 12) +(in nt, default 9) .TP \fB\-\-canonical\-mode\fR=\fI\,INT\/\fR Reward for canonical and semi\-canonical introns @@ -138,7 +139,7 @@ Allow an insertion and deletion close to each other .TP \fB\-\-microexon\-spliceprob\fR=\fI\,FLOAT\/\fR Allow microexons only if one of the splice site probabilities is -greater than this value (default 0.90) +greater than this value (default 0.95) .TP \fB\-\-cmetdir\fR=\fI\,STRING\/\fR Directory for methylcytosine index files (created using cmetindex) @@ -156,7 +157,7 @@ to have previously run the cmetindex or atoiindex programs on the genome \fB\-p\fR, \fB\-\-prunelevel\fR Pruning level: 0=no pruning (default), 1=poor seqs, 2=repetitive seqs, 3=poor and repetitive -.SS +.PP Output types .TP \fB\-S\fR, \fB\-\-summary\fR @@ -185,7 +186,7 @@ Print protein sequence (genomic) .TP \fB\-f\fR, \fB\-\-format\fR=\fI\,INT\/\fR Other format for output (also note the \fB\-A\fR and \fB\-S\fR options -and other options listed under Output types): + 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, @@ -197,7 +198,7 @@ and other options listed under Output types): 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 +.PP Output options .TP \fB\-n\fR, \fB\-\-npaths\fR=\fI\,INT\/\fR @@ -265,7 +266,13 @@ Implies \fB\-F\fR flag. .TP \fB\-Y\fR, \fB\-\-tolerant\fR Translates cDNA with corrections for frameshifts -.SS +.PP +Options for GFF3 output +.TP +\fB\-\-gff3\-add\-separators\fR=\fI\,INT\/\fR +Whether to add a ### separator after each query sequence +Values: 0 (no), 1 (yes, default) +.PP Options for SAM output .TP \fB\-\-no\-sam\-headers\fR @@ -287,6 +294,10 @@ In MD string, when known SNPs are given by the \fB\-v\fR flag, prints difference nucleotides as lower\-case when they, differ from reference but match a known alternate allele .TP +\fB\-\-action\-if\-cigar\-error\fR +Action to take if there is a disagreement between CIGAR length and sequence length +Allowed values: ignore, warning (default), abort +.TP \fB\-\-read\-group\-id\fR=\fI\,STRING\/\fR Value to put into read\-group id (RG\-ID) field .TP @@ -298,23 +309,24 @@ Value to put into read\-group library (RG\-LB) field .TP \fB\-\-read\-group\-platform\fR=\fI\,STRING\/\fR Value to put into read\-group library (RG\-PL) field -.SS +.PP Options for quality scores .TP \fB\-\-quality\-protocol\fR=\fI\,STRING\/\fR Protocol for input quality scores. Allowed values: - illumina (ASCII 64\-126) (equivalent to \fB\-J\fR 64 \fB\-j\fR \fB\-31\fR) - sanger (ASCII 33\-126) (equivalent to \fB\-J\fR 33 \fB\-j\fR 0) - +illumina (ASCII 64\-126) (equivalent to \fB\-J\fR 64 \fB\-j\fR \fB\-31\fR) +sanger (ASCII 33\-126) (equivalent to \fB\-J\fR 33 \fB\-j\fR 0) +.TP Default is sanger (no quality print shift) SAM output files should have quality scores in sanger protocol +.IP Or you can specify the print shift with this flag: .TP \fB\-j\fR, \fB\-\-quality\-print\-shift\fR=\fI\,INT\/\fR Shift FASTQ quality scores by this amount in output (default is 0 for sanger protocol; to change Illumina input to Sanger output, select \fB\-31\fR) -.SS +.PP External map file options .TP \fB\-M\fR, \fB\-\-mapdir\fR=\fI\,directory\/\fR @@ -335,7 +347,7 @@ Show flanking hits (default 0) .TP \fB\-\-print\-comment\fR Show comment line for each hit -.SS +.PP Alignment output options .TP \fB\-N\fR, \fB\-\-nolengths\fR @@ -348,11 +360,11 @@ Mode for alignments to genomic (\-) strand: 2=Invert cDNA and print genomic (+) strand .TP \fB\-i\fR, \fB\-\-introngap\fR=\fI\,INT\/\fR -Nucleotides to show on each end of intron (default=3) +Nucleotides to show on each end of intron (default 3) .TP \fB\-l\fR, \fB\-\-wraplength\fR=\fI\,INT\/\fR -Wrap length for alignment (default=50) -.SS +Wrap length for alignment (default 50) +.PP Filtering output options .TP \fB\-\-min\-trimmed\-coverage\fR=\fI\,FLOAT\/\fR @@ -366,7 +378,7 @@ Do not print alignments with identity less this value (default=0.0, which means no filtering) Note that chimeric alignments will be output regardless of this filter -.SS +.PP Help options .TP \fB\-\-version\fR diff --git a/debian/gmap_build.1 b/debian/gmap_build.1 index 5252109..46f3e5e 100644 --- a/debian/gmap_build.1 +++ b/debian/gmap_build.1 @@ -1,4 +1,4 @@ -.TH GMAP_BUILD "1" "GMAP 2014-10-22" "User Commands" +.TH GMAP_BUILD "1" "GMAP 2014-12-23" "User Commands" .SH NAME gmap_build \- create a genome database for GMAP or GSNAP .SH SYNOPSIS @@ -6,11 +6,20 @@ gmap_build \- create a genome database for GMAP or GSNAP [\fI\,options\/\fR...] \fI\,-d <genomename> <fasta_files>\/\fR .SH DESCRIPTION .PP -gmap_build: - Builds a gmap database for a genome to be used by GMAP or GSNAP. - Part of GMAP package, version 2014\-07\-28. - Starting from version 2013-10-28, gmap_setup program is removed, now supporting only gmap_build. - Moved options from gmap_setup to gmap_build. +.SH NAME +gmap_build \- manual page for gmap_build 2014 +.SH SYNOPSIS +.B gmap_build +[\fI\,options\/\fR...] \fI\,-d <genomename> <fasta_files>\/\fR +.SH DESCRIPTION +Unknown option: help +\fB\-k\fR flag not specified, so building with default 15\-mers +Must specify genome database name with \fB\-d\fR flag. at \fI\,/usr/bin/gmap_build\/\fP line 67. +.PP +gmap_build: Builds a gmap database for a genome to be used by GMAP or GSNAP. +Part of GMAP package, version 2014\-12\-23. +.PP +A simplified alternative to using the program gmap_setup, which creates a Makefile. .SH OPTIONS .TP \fB\-D\fR, \fB\-\-dir\fR=\fI\,STRING\/\fR @@ -90,4 +99,3 @@ Copyright 2005 Genentech, Inc. All rights reserved. \fBgmap\fR(1), \fBgsnap\fR(1) .br http://research-pub.gene.com/gmap/ - diff --git a/debian/gsnap.1 b/debian/gsnap.1 index 2fa49d5..3924169 100644 --- a/debian/gsnap.1 +++ b/debian/gsnap.1 @@ -1,4 +1,4 @@ -.TH GSNAP "1" "GMAP 2014-10-22" "User Commands" +.TH GSNAP "1" "GMAP 2014-12-23" "User Commands" .SH NAME gsnap \- Genomic Short-read Nucleotide Alignment Program .SH SYNOPSIS @@ -9,14 +9,16 @@ gsnap \- Genomic Short-read Nucleotide Alignment Program Input options (must include \fB\-d\fR) .TP \fB\-D\fR, \fB\-\-dir\fR=\fI\,directory\/\fR -Genome directory +Genome directory. Default (as specified by \fB\-\-with\-gmapdb\fR to the configure program) is +\fI\,/var/cache/gmap\/\fP .TP \fB\-d\fR, \fB\-\-db\fR=\fI\,STRING\/\fR Genome database .TP \fB\-\-use\-sarray\fR=\fI\,INT\/\fR Whether to use a suffix array, which will give increased speed. -Allowed values: 0 (no) or 1 (yes, if available, default). +Allowed values: 0 (no), 1 (yes, plus GSNAP/GMAP algorithm, default), +or 2 (yes, and use only suffix array algorithm). Note that suffix arrays will bias against SNP alleles in SNP\-tolerant alignment. .TP @@ -77,13 +79,11 @@ on both ends of a paired\-end read (or on the only end of a single\-end read). .TP \fB\-\-allow\-pe\-name\-mismatch\fR Allows accession names of reads to mismatch in paired\-end files -.TP -\fB\-\-gunzip\fR -Uncompress gzipped input files -.SS +.PP Computation options .IP Note: GSNAP has an ultrafast algorithm for calculating mismatches up to and including +.PP ((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 @@ -98,6 +98,7 @@ is still designed to be fast. 3 see note allocate mmap & preload mmap & preload 4 see note allocate allocate mmap & preload 5 see note allocate allocate allocate + 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 @@ -140,9 +141,7 @@ Reducing this number can speed up the program. .TP \fB\-\-terminal\-threshold\fR=\fI\,INT\/\fR Threshold for computing a terminal alignment (from one end of the -read to the best possible position at the other end) (default 2 -for standard, atoi\-stranded, and atoi\-nonstranded mode; -default 1000 for cmet\-stranded and cmet\-nonstranded mode). +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. To turn off the computation of terminal alignments, set this to a @@ -152,13 +151,13 @@ find some alignments. Therefore, to avoid getting terminal alignments in the output, you should generally set \fB\-\-terminal\-output\-minlength\fR instead of this parameter. .TP -\fB\-\-terminal\-output\-minlength\fR=\fI\,INT\/\fR -Threshold alignment length in bp for a terminal alignment result to be printed +\fB\-\-reject\-trimlength\fR=\fI\,INT\/\fR +Do not print alignments where amount trimmed on both ends totals more than .TP -(in bp) (default 25 for RNA\-Seq standard, atoi\-stranded, and atoi\-nonstranded modes; -default MAX_READLENGTH for other RNA\-Seq modes and for DNA\-Seq in all modes). -Setting this parameter to a value of MAX_READLENGTH or more will prevent -all terminal alignments from being printed. +this amount (default 1000). +Note that ambiguous splicing does not count +.IP +as a trim. .TP \fB\-i\fR, \fB\-\-indel\-penalty\fR=\fI\,INT\/\fR Penalty for an indel (default 2). @@ -195,7 +194,7 @@ 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=\fI\,INT\/\fR -Score to use for indels when trimming at ends (default is \fB\-4\fR; +Score to use for indels when trimming at ends (default is \fB\-2\fR; to turn off trimming, specify 0). Warning: turning trimming off will give false positive indels at the ends of reads .TP @@ -238,7 +237,7 @@ Use this runlength IIT file to resolve concordant multiple results .TP \fB\-t\fR, \fB\-\-nthreads\fR=\fI\,INT\/\fR Number of worker threads -.SS +.PP Options for GMAP alignment within GSNAP .TP \fB\-\-gmap\-mode\fR=\fI\,STRING\/\fR @@ -260,11 +259,11 @@ Extra mismatch/indel score allowed for GMAP alignments (default 3) .TP \fB\-\-max\-gmap\-pairsearch\fR=\fI\,INT\/\fR Perform GMAP pairsearch on nearby genomic regions up to this many -many candidate ends (default 10). Requires pairsearch in \fB\-\-gmap\-mode\fR +many candidate ends (default 50). Requires pairsearch in \fB\-\-gmap\-mode\fR .TP \fB\-\-max\-gmap\-terminal\fR=\fI\,INT\/\fR Perform GMAP terminal on nearby genomic regions up to this many -candidate ends (default 5). Requires terminal in \fB\-\-gmap\-mode\fR +candidate ends (default 50). Requires terminal in \fB\-\-gmap\-mode\fR .TP \fB\-\-max\-gmap\-improvement\fR=\fI\,INT\/\fR Perform GMAP improvement on nearby genomic regions up to this many @@ -272,8 +271,8 @@ candidate ends (default 5). Requires improve in \fB\-\-gmap\-mode\fR .TP \fB\-\-microexon\-spliceprob\fR=\fI\,FLOAT\/\fR Allow microexons only if one of the splice site probabilities is -greater than this value (default 0.90) -.SS +greater than this value (default 0.95) +.PP Splicing options for RNA\-Seq .TP \fB\-N\fR, \fB\-\-novelsplicing\fR=\fI\,INT\/\fR @@ -325,7 +324,7 @@ need the end length to be the value of \fB\-k\fR, or kmer size to find a given s Minimum identity at end required for distant spliced alignments (default 0.95) .TP \fB\-\-antistranded\-penalty\fR=\fI\,INT\/\fR -(Not currently implemented) +(Not currently implemented, since it leads to poor results) 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 @@ -335,7 +334,7 @@ equally well 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 +.PP Options for paired\-end reads .TP \fB\-\-pairmax\-dna\fR=\fI\,INT\/\fR @@ -348,13 +347,13 @@ that could have a splice (default 200000). Used if \fB\-N\fR or \fB\-s\fR is sp Should probably match the value for \fB\-w\fR, \fB\-\-localsplicedist\fR. .TP \fB\-\-pairexpect\fR=\fI\,INT\/\fR -Expected paired\-end length, used for calling splices in medial part of -paired\-end reads (default 200) +Expected paired\-end length, previously used for calling splices in medial part +of paired\-end reads (default 200). Currently not used. .TP \fB\-\-pairdev\fR=\fI\,INT\/\fR -Allowable deviation from expected paired\-end length, used for -calling splices in medial part of paired\-end reads (default 100) -.SS +Allowable deviation from expected paired\-end length, previously used for +calling splices in medial part of paired\-end reads (default 100). Currently not used. +.PP Options for quality scores .TP \fB\-\-quality\-protocol\fR=\fI\,STRING\/\fR @@ -362,10 +361,10 @@ Protocol for input quality scores. Allowed values: illumina (ASCII 64\-126) (equivalent to \fB\-J\fR 64 \fB\-j\fR \fB\-31\fR) sanger (ASCII 33\-126) (equivalent to \fB\-J\fR 33 \fB\-j\fR 0) - +.TP Default is sanger (no quality print shift) SAM output files should have quality scores in sanger protocol - +.IP Or you can customize this behavior with these flags: .TP \fB\-J\fR, \fB\-\-quality\-zero\-score\fR=\fI\,INT\/\fR @@ -376,7 +375,7 @@ 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 \fB\-31\fR) -.SS +.PP Output options .TP \fB\-n\fR, \fB\-\-npaths\fR=\fI\,INT\/\fR @@ -398,6 +397,9 @@ all differences relative to both the reference and alternate genome) \fB\-\-clip\-overlap\fR For paired\-end reads whose alignments overlap, clip the overlapping region. .TP +\fB\-\-merge\-overlap\fR +For paired\-end reads whose alignments overlap, merge the two ends into a single end (beta implementation) +.TP \fB\-\-print\-snps\fR Print detailed information about SNPs in reads (works only if \fB\-v\fR also selected) (not fully implemented yet) @@ -410,7 +412,7 @@ Exclude printing of failed alignments .TP \fB\-A\fR, \fB\-\-format\fR=\fI\,STRING\/\fR Another format type, other than default. -Currently implemented: sam +Currently implemented: sam, m8 (BLAST tabular format) Also allowed, but not installed at compile\-time: goby (To install, need to re\-compile with appropriate options) .TP @@ -429,11 +431,15 @@ in addition to the output in the .nomapping file. When \fB\-\-split\-output\fR or \fB\-\-failed\-input\fR is given, this flag will append output to the existing files. Otherwise, the default is to create new files. .TP +\fB\-\-order\-among\-best\fR=\fI\,STRING\/\fR +Among alignments tied with the best score, order those alignments in this order. +Allowed values: genomic, random (default) +.TP \fB\-\-output\-buffer\-size\fR=\fI\,INT\/\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 +.PP Options for SAM output .TP \fB\-\-no\-sam\-headers\fR @@ -462,6 +468,13 @@ In MD string, when known SNPs are given by the \fB\-v\fR flag, prints difference nucleotides as lower\-case when they, differ from reference but match a known alternate allele .TP +\fB\-\-extend\-soft\-clips\fR +Extends alignments through soft clipped regions +.TP +\fB\-\-action\-if\-cigar\-error\fR +Action to take if there is a disagreement between CIGAR length and sequence length +Allowed values: ignore, warning (default), abort +.TP \fB\-\-read\-group\-id\fR=\fI\,STRING\/\fR Value to put into read\-group id (RG\-ID) field .TP @@ -473,7 +486,7 @@ Value to put into read\-group library (RG\-LB) field .TP \fB\-\-read\-group\-platform\fR=\fI\,STRING\/\fR Value to put into read\-group library (RG\-PL) field -.SS +.PP Help options .TP \fB\-\-version\fR -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gmap.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
