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commit ffd9490012a03bcc1e8197e04cb06769400336a0 Author: Afif Elghraoui <a...@ghraoui.name> Date: Wed Jul 29 22:09:49 2015 -0700 Combine the two blasr help files into one manpage --- debian/{blasr.1.second => blasr.1} | 64 ++++++++++++++++++++++++++++++++-- debian/blasr.1.first | 70 -------------------------------------- 2 files changed, 61 insertions(+), 73 deletions(-) diff --git a/debian/blasr.1.second b/debian/blasr.1 similarity index 80% rename from debian/blasr.1.second rename to debian/blasr.1 index ccee73e..cd2f279 100644 --- a/debian/blasr.1.second +++ b/debian/blasr.1 @@ -1,9 +1,67 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4. -.TH BLASR "1" "July 2015" "blasr git1dlkf23" "User Commands" +.TH BLASR "1" "July 2015" "blasr 3ca7fe8" "User Commands" .SH NAME -blasr \- program description goes here +blasr \- Map SMRT Sequences to a reference genome. +.SH SYNOPSIS +.IP +blasr reads.bam genome.fasta \fB\-bam\fR \fB\-out\fR out.bam +.IP +blasr reads.fasta genome.fasta +.IP +blasr reads.fasta genome.fasta \fB\-sa\fR genome.fasta.sa +.IP +blasr reads.bax.h5 genome.fasta [\-sa genome.fasta.sa] +.IP +blasr reads.bax.h5 genome.fasta \fB\-sa\fR genome.fasta.sa \fB\-maxScore\fR \fB\-100\fR \fB\-minMatch\fR 15 ... +.IP +blasr reads.bax.h5 genome.fasta \fB\-sa\fR genome.fasta.sa \fB\-nproc\fR 24 \fB\-out\fR alignment.out ... .SH DESCRIPTION .IP +blasr is a read mapping program that maps reads to positions +in a genome by clustering short exact matches between the read and +the genome, and scoring clusters using alignment. The matches are +generated by searching all suffixes of a read against the genome +using a suffix array. Global chaining methods are used to score +clusters of matches. +.IP +The only required inputs to blasr are a file of reads and a +reference genome. It is exremely useful to have read filtering +information, and mapping runtime may decrease substantially when a +precomputed suffix array index on the reference sequence is +specified. +.IP +Although reads may be input in FASTA format, the recommended input is +PacBio BAM files because these contain qualtiy value +information that is used in the alignment and produces higher quality +variant detection. +Although alignments can be output in various formats, the recommended +output format is PacBio BAM. +Support to bax.h5 and plx.h5 files will be DEPRECATED. +Support to region tables for h5 files will be DEPRECATED. +.IP +When suffix array index of a genome is not specified, the suffix array is +built before producing alignment. This may be prohibitively slow +when the genome is large (e.g. Human). It is best to precompute the +suffix array of a genome using the program sawriter, and then specify +the suffix array on the command line using \fB\-sa\fR genome.fa.sa. +.IP +The optional parameters are roughly divided into three categories: +control over anchoring, alignment scoring, and output. +.IP +The default anchoring parameters are optimal for small genomes and +samples with up to 5% divergence from the reference genome. The main +parameter governing speed and sensitivity is the \fB\-minMatch\fR parameter. +For human genome alignments, a value of 11 or higher is recommended. +Several methods may be used to speed up alignments, at the expense of +possibly decreasing sensitivity. +.IP +Regions that are too repetitive may be ignored during mapping by +limiting the number of positions a read maps to with the +\fB\-maxAnchorsPerPosition\fR option. Values between 500 and 1000 are effective +in the human genome. +.IP +For small genomes such as bacterial genomes or BACs, the default parameters +are sufficient for maximal sensitivity and good speed. +.SH OPTIONS Options for blasr Basic usage: 'blasr reads.{bam|fasta|bax.h5|fofn} genome.fasta [\-options] .IP diff --git a/debian/blasr.1.first b/debian/blasr.1.first deleted file mode 100644 index 58ab9c2..0000000 --- a/debian/blasr.1.first +++ /dev/null @@ -1,70 +0,0 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4. -.TH BLASR "1" "July 2015" "blasr 3ca7fe8" "User Commands" -.SH NAME -blasr \- program description goes here -.SH DESCRIPTION -NAME -.IP -blasr \- Map SMRT Sequences to a reference genome. -.PP -SYNOPSIS -.IP -blasr reads.bam genome.fasta \fB\-bam\fR \fB\-out\fR out.bam -.IP -blasr reads.fasta genome.fasta -.IP -blasr reads.fasta genome.fasta \fB\-sa\fR genome.fasta.sa -.IP -blasr reads.bax.h5 genome.fasta [\-sa genome.fasta.sa] -.IP -blasr reads.bax.h5 genome.fasta \fB\-sa\fR genome.fasta.sa \fB\-maxScore\fR \fB\-100\fR \fB\-minMatch\fR 15 ... -.IP -blasr reads.bax.h5 genome.fasta \fB\-sa\fR genome.fasta.sa \fB\-nproc\fR 24 \fB\-out\fR alignment.out ... -.PP -DESCRIPTION -.IP -blasr is a read mapping program that maps reads to positions -in a genome by clustering short exact matches between the read and -the genome, and scoring clusters using alignment. The matches are -generated by searching all suffixes of a read against the genome -using a suffix array. Global chaining methods are used to score -clusters of matches. -.IP -The only required inputs to blasr are a file of reads and a -reference genome. It is exremely useful to have read filtering -information, and mapping runtime may decrease substantially when a -precomputed suffix array index on the reference sequence is -specified. -.IP -Although reads may be input in FASTA format, the recommended input is -PacBio BAM files because these contain qualtiy value -information that is used in the alignment and produces higher quality -variant detection. -Although alignments can be output in various formats, the recommended -output format is PacBio BAM. -Support to bax.h5 and plx.h5 files will be DEPRECATED. -Support to region tables for h5 files will be DEPRECATED. -.IP -When suffix array index of a genome is not specified, the suffix array is -built before producing alignment. This may be prohibitively slow -when the genome is large (e.g. Human). It is best to precompute the -suffix array of a genome using the program sawriter, and then specify -the suffix array on the command line using \fB\-sa\fR genome.fa.sa. -.IP -The optional parameters are roughly divided into three categories: -control over anchoring, alignment scoring, and output. -.IP -The default anchoring parameters are optimal for small genomes and -samples with up to 5% divergence from the reference genome. The main -parameter governing speed and sensitivity is the \fB\-minMatch\fR parameter. -For human genome alignments, a value of 11 or higher is recommended. -Several methods may be used to speed up alignments, at the expense of -possibly decreasing sensitivity. -.IP -Regions that are too repetitive may be ignored during mapping by -limiting the number of positions a read maps to with the -\fB\-maxAnchorsPerPosition\fR option. Values between 500 and 1000 are effective -in the human genome. -.IP -For small genomes such as bacterial genomes or BACs, the default parameters -are sufficient for maximal sensitivity and good speed. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/blasr.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit