[med-svn] [gmap] 07/08: d/*.1: updated man pages
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Fri Mar 13 09:51:50 UTC 2015
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository gmap.
commit 09015de408e84888f68370f581b271103e95bb1e
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
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
--
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