[med-svn] [blat] 02/03: Two additional manpages added using edited help2man output

[Andreas Tille]

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tille pushed a commit to branch master
in repository blat.

commit ebb8a41f3c92e3a629b36d84354a2f56072fc83b
Author: Andreas Tille <tille at debian.org>
Date:   Mon Mar 3 10:18:59 2014 +0100

    Two additional manpages added using edited help2man output
---
 debian/mans/nibFrag.1   | 29 +++++++++++++++++++++++++++++
 debian/mans/pslPretty.1 | 31 +++++++++++++++++++++++++++++++
 2 files changed, 60 insertions(+)

diff --git a/debian/mans/nibFrag.1 b/debian/mans/nibFrag.1
new file mode 100644
index 0000000..efe6f13
--- /dev/null
+++ b/debian/mans/nibFrag.1
@@ -0,0 +1,29 @@
+.TH NIBFRAG "1" "February 2014" "nibFrag 35" "User Commands"
+.SH NAME
+nibFrag \- Extract part of a nib file as .fa
+.SH SYNOPSIS
+.B nibFrag
+\fI[options]\fR file.nib start end strand out.fa
+.SH DESCRIPTION
+.P
+Blat is an alignment tool like BLAST, but it is structured differently.
+The target database of BLAT is not  a  set  of  GenBank  sequences,  but
+instead an index derived from the assembly of the entire genome.
+.P
+The command line tool \fBnibFrag\fR extracts part of a nib file as .fa
+(all bases/gaps lower case by default)
+.SH OPTIONS
+.HP
+\fBstrand\fR \- + (plus) or m (minus)
+.HP
+\fB\-masked\fR \- use lower case characters for bases meant to be masked out
+.HP
+\fB\-hardMasked\fR \- use upper case for not masked\-out and 'N' characters for masked\-out bases
+.HP
+\fB\-upper\fR \- use upper case characters for all bases
+.HP
+\fB\-name\fR=\fIname\fR Use given name after '>' in output sequence
+.HP
+\fB\-dbHeader\fR=\fIdb\fR Add full database info to the header, with or without \fB\-name\fR option
+.HP
+\fB\-tbaHeader\fR=\fIdb\fR Format header for compatibility with tba, takes database name as argument
diff --git a/debian/mans/pslPretty.1 b/debian/mans/pslPretty.1
new file mode 100644
index 0000000..3acb692
--- /dev/null
+++ b/debian/mans/pslPretty.1
@@ -0,0 +1,31 @@
+.TH PSLPRETTY "1" "February 2014" "pslPretty 35" "User Commands"
+.SH NAME
+pslPretty \- Convert PSL to human readable output
+.SH SYNOPSIS
+.B pslPretty
+in.psl target.lst query.lst pretty.out
+.SH DESCRIPTION
+.P
+Blat is an alignment tool like BLAST, but it is structured differently.
+The target database of BLAT is not  a  set  of  GenBank  sequences,  but
+instead an index derived from the assembly of the entire genome.
+.P
+The command line tool \fBpslPretty\fR converts PSL to human readable output.
+.SH OPTIONS
+.TP
+\fB\-axt\fR \- save in something like Scott Schwartz's axt format
+.IP
+Note gaps in both sequences are still allowed in the
+output which not all axt readers will expect
+.HP
+\fB\-dot\fR=\fIN\fR Put out a dot every N records
+.HP
+\fB\-long\fR \- Don't abbreviate long inserts
+.HP
+\fB\-check\fR=\fIfileName\fR \- Output alignment checks to filename
+.IP
+It's a really good idea if the psl file is sorted by target
+if it contains multiple targets.  Otherwise this will be
+very very slow.   The target and query lists can either be
+fasta, 2bit or nib files, or a list of fasta, 2bit and/or nib files
+one per line

-- 
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