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commit 9734970953ad3f0bbb0cb160f8fdf3a8287f806e
Author: Afif Elghraoui <a...@ghraoui.name>
Date: Thu Jul 30 00:11:43 2015 -0700
Finalize manpage for samFilter
---
debian/samFilter.1 | 175 ++++++++++++++++++++++++++---------------------------
1 file changed, 85 insertions(+), 90 deletions(-)
diff --git a/debian/samFilter.1 b/debian/samFilter.1
index dc0aab8..2409bd6 100644
--- a/debian/samFilter.1
+++ b/debian/samFilter.1
@@ -1,130 +1,125 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
.TH SAMFILTER "1" "July 2015" "samFilter 3ca7fe8" "User Commands"
.SH NAME
-samFilter \- description of program
-.SH DESCRIPTION
-usage: [file.sam] [reference.fasta] [out.sam] [options]
-.IP
-file.sam
-.IP
+samFilter \- filter nucleotide sequence alignments in SAM files
+.SH SYNOPSIS
+.B samFilter
+.I file.sam
+.I reference.fasta
+.I out.sam
+.RI [ options ]
+.SH OPTIONS
+.TP
+.I file.sam
Input SAM file.
-.IP
-reference.fasta
-.IP
+.TP
+.I reference.fasta
Reference used to generate reads.
-.IP
-out.sam
-.IP
+.TP
+.I out.sam
Output SAM file.
-.HP
-\fB\-minAlnLength\fR value
-.IP
+.TP
+.BI \-minAlnLength \0value
(50) Report alignments only if their lengths are greater than
-minAlnLength.
-.HP
-\fB\-minAlignLength\fR value
-.IP
+\fIvalue\fR.
+.TP
+.BI \-minAlignLength \0value
Alias of \fB\-minAlnLength\fR
-.HP
-\fB\-minLength\fR value
-.IP
+.TP
+.BI \-minLength \0value
Alias of \fB\-minAlnLength\fR
-.HP
-\fB\-minPctSimilarity\fR value
+.TP
+.BI \-minPctSimilarity \0value
.IP
(70) Report alignments only if their percentage similairty is
-greater than minPctSimilarity.
-.HP
-\fB\-minPctIdentity\fR value
-.IP
+greater than \fIvalue\0.
+.TP
+.BI \-minPctIdentity \0value
Alias of \fB\-minPctSimilarity\fR
-.HP
-\fB\-minPctAccuracy\fR value
-.IP
+.TP
+.BI \-minPctAccuracy \0value
(70) Report alignments only if their percentage accuray is
-greater than minAccuracy.
-.HP
-\fB\-minAccuracy\fR value
-.IP
+greater than \fIvalue\fR.
+.TP
+.BI \-minAccuracy \0value
Alias of \fB\-minPctAccuracy\fR
-.HP
-\fB\-hitPolicy\fR value
-.IP
+.TP
+.BI \-hitPolicy \0value
(randombest) Specify a policy to treat multiple hits from [all,
allbest, random, randombest, leftmost]
+.RS
.TP
-all
-: report all alignments.
+.I all
+report all alignments.
.TP
-allbest
-: report all equally top scoring alignments.
+.I allbest
+report all equally top scoring alignments.
.TP
-random
-: report a random alignment.
-.IP
-randombest: report a random alignment from multiple equally
-.IP
-top scoring alignments.
+.I random
+report a random alignment.
.TP
-leftmost
-: report an alignment which has the best
-.IP
-alignmentscore and has the smallest mapping coordinate in any
-reference.
-.HP
-\fB\-scoreSign\fR value
-.IP
-(\fB\-1\fR) Whether higher or lower scores are better. \fB\-1\fR: lower is
-better; 1: higher is better.
-.HP
-\fB\-scoreCutoff\fR value
-.IP
+.I randombest
+report a random alignment from multiple equally top scoring alignments.
+.TP
+.I leftmost
+report an alignment which has the best alignmentscore and has the smallest
+mapping coordinate in any reference.
+.RE
+.TP
+.BI \-scoreSign \0value
+(\-1) Whether higher or lower scores are better.
+.RS
+.TP
+\-1
+lower is better
+.TP
+1
+higher is better.
+.RE
+.TP
+.BI \-scoreCutoff \0value
(INF) Report alignments only if their scores are no worse than
-score cut off.
-.HP
-\fB\-seed\fR value
+\fIvalue\fR.
.TP
-(1)
-Seed for random number generator.
-.IP
+.BI \-seed \0value
+(1) Seed for random number generator.
If seed is 0, then use current time as seed.
-.HP
-\fB\-holeNumbers\fR value
-.IP
-A string of comma\-delimited hole number ranges to output hits,
-such as '1,2,10\-12'. This requires hit titles to be in SMRT read
+.TP
+.BI \-holeNumbers \0value
+A string of comma-delimited hole number ranges to output hits,
+such as '1,2,10-12'. This requires hit titles to be in SMRT read
title format.
-.HP
-\fB\-smrtTitle\fR
-.IP
+.TP
+.B \-smrtTitle
Use this option when filtering alignments generated by programs
-other than blasr, e.g. bwa\-sw or gmap. Parse read coordinates
+other than
+.BR blasr (1),
+e.g. bwa\-sw or gmap. Parse read coordinates
from the SMRT read title. The title is in the format
\fI\,/name/hole/coordinates\/\fP, where coordinates are in the format
\ed+_\ed+, and represent the interval of the read that was
aligned.
-.HP
-\fB\-titleTable\fR value
-.IP
+.TP
+.BI \-titleTable \0value
Use this experimental option when filtering alignments generated
-by blasr with \fB\-titleTable\fR titleTableName, in which case
+by
+.BR blasr (1)
+with \fB\-titleTable\fR titleTableName, in which case
reference titles in SAM are represented by their indices (e.g.,
0, 1, 2, ...) in the title table.
-.HP
-\fB\-filterAdapterOnly\fR value
-.IP
+.TP
+.BI \-filterAdapterOnly \0value
Use this option to remove reads which can only map to adapters
specified in the GFF file.
-.HP
-\fB\-v\fR
-.IP
+.TP
+.B \-v
Be verbose.
-.IP
+.SH NOTES
Because SAM has optional tags that have different meanings in different
programs, careful usage is required in order to have proper output. The
"xs" tag in bwa\-sw is used to show the suboptimal score, but in PacBio SAM
-(blasr) it is defined as the start in the query sequence of the alignment.
-When "\-smrtTitle" is specified, the xs tag is ignored, but when it is not
+.RB ( blasr (1))
+it is defined as the start in the query sequence of the alignment.
+When \fB\-smrtTitle\fR is specified, the xs tag is ignored, but when it is not
specified, the coordinates given by the xs and xe tags are used to define
the interval of a read that is aligned. The CIGAR string is relative to
this interval.
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