[med-svn] [libfastahack] 02/04: Add manpage

[Andreas Tille]

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commit e2caddfaf6605d32ae42ff156f50769d04fee5f4
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jun 23 13:51:37 2016 +0200

    Add manpage
---
 debian/fastahack.1 | 60 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 debian/manpages    |  1 +
 2 files changed, 61 insertions(+)

diff --git a/debian/fastahack.1 b/debian/fastahack.1
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index 0000000..edc2d87
--- /dev/null
+++ b/debian/fastahack.1
@@ -0,0 +1,60 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH FASTAHACK "1" "June 2016" "fastahack 0.0+20160309" "User Commands"
+.SH NAME
+fastahack \- indexing and sequence extraction from FASTA files
+.SH SYNOPSIS
+.B fastahack
+[options] <fasta reference>
+.SH DESCRIPTION
+fastahack is a small application for indexing and extracting sequences and
+subsequences from FASTA files.  The included Fasta.cpp library provides a FASTA
+reader and indexer that can be embedded into applications which would benefit
+from directly reading subsequences from FASTA files.  The library automatically
+handles index file generation and use.
+.P
+Features:
+.IP
+FASTA index (.fai) generation for FASTA files
+.IP
+Sequence extraction
+.IP
+Subsequence extraction
+.IP
+Sequence statistics (currently only entropy is provided)
+.P
+Sequence and subsequence extraction use fseek64 to provide fastest-possible
+extraction without RAM-intensive file loading operations.  This makes fastahack
+a useful tool for bioinformaticists who need to quickly extract many
+subsequences from a reference FASTA sequence.
+.SH OPTIONS
+.TP
+\fB\-i\fR, \fB\-\-index\fR
+generate fasta index <fasta reference>.fai
+.TP
+\fB\-r\fR, \fB\-\-region\fR REGION
+print the specified region
+.TP
+\fB\-c\fR, \fB\-\-stdin\fR
+read a stream of line\-delimited region specifiers on stdin
+and print the corresponding sequence for each on stdout
+.TP
+\fB\-e\fR, \fB\-\-entropy\fR
+print the shannon entropy of the specified region
+.TP
+\fB\-d\fR, \fB\-\-dump\fR
+print the fasta file in the form 'seq_name <tab> sequence'
+.P
+REGION is of the form
+.IP
+<seq>, <seq>:<start>[sep]<end>, <seq1>:<start>[sep]<seq2>:<end>
+.P
+where start and end are 1\-based, and the region includes the end position.
+[sep] is "\-" or ".."
+.PP
+Specifying a sequence name alone will return the entire sequence, specifying
+range will return that range, and specifying a single coordinate pair, e.g.
+<seq>:<start> will return just that base.
+.SH AUTHOR
+This software was written by Erik Garrison <erik.garrison at bc.edu>.
+.P
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/manpages b/debian/manpages
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+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1

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