[med-svn] [blasr] 02/12: Combine the two blasr help files into one manpage

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
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commit ffd9490012a03bcc1e8197e04cb06769400336a0
Author: Afif Elghraoui <afif at 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.

-- 
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