[med-svn] r19044 - trunk/packages/mummer/trunk/debian

[Andreas Tille]

Author: tille
Date: 2015-04-14 07:34:14 +0000 (Tue, 14 Apr 2015)
New Revision: 19044

Added:
   trunk/packages/mummer/trunk/debian/delta2blocks.1
Modified:
   trunk/packages/mummer/trunk/debian/mummer.links
   trunk/packages/mummer/trunk/debian/mummer.manpages
Log:
Manpage for additional tools


Added: trunk/packages/mummer/trunk/debian/delta2blocks.1
===================================================================
--- trunk/packages/mummer/trunk/debian/delta2blocks.1	                        (rev 0)
+++ trunk/packages/mummer/trunk/debian/delta2blocks.1	2015-04-14 07:34:14 UTC (rev 19044)
@@ -0,0 +1,39 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH DELTA2BLOCKS "1" "April 2015" "delta2blocks 3.23" "User Commands"
+.SH NAME
+delta2blocks \- extra tool for mummer from patch of mugsy to sort alignments
+.br
+delta2maf \- extra tool for mummer from patch of mugsy to sort alignments
+.SH SYNOPSIS
+.B delta2blocks
+.RI [options]  <deltafile>  <ref ID>  <qry ID>
+.br
+.B delta2maf
+.RI [options]  <deltafile>  <ref ID>  <qry ID>
+.SH DESCRIPTION
+.TP
+\fB\-h\fR            Display help information
+.TP
+\fB\-q\fR            Sort alignments by the query start coordinate
+.TP
+\fB\-r\fR            Sort alignments by the reference start coordinate
+.TP
+\fB\-w\fR int        Set the screen width \- default is 60
+.TP
+\fB\-x\fR int        Set the matrix type \- default is 2 (BLOSUM 62),
+.PP
+other options include 1 (BLOSUM 45) and 3 (BLOSUM 80)
+note: only has effect on amino acid alignments
+.PP
+Input is the .delta output of either the "nucmer" or the
+"promer" program passed on the command line.
+.PP
+Output is to stdout, and consists of all the alignments between the
+query and reference sequences identified on the command line.
+.PP
+NOTE: No sorting is done by default, therefore the alignments
+will be ordered as found in the <deltafile> input.
+.SH SEE ALSO
+This tool originates from mugsy that provides a code copy of mummer
+with additional patches.  The source can be found in SVN
+svn://svn.code.sf.net/p/mugsy/code/trunk
\ No newline at end of file

Modified: trunk/packages/mummer/trunk/debian/mummer.links
===================================================================
--- trunk/packages/mummer/trunk/debian/mummer.links	2015-04-14 06:34:01 UTC (rev 19043)
+++ trunk/packages/mummer/trunk/debian/mummer.links	2015-04-14 07:34:14 UTC (rev 19044)
@@ -17,3 +17,4 @@
 usr/share/man/man1/mummer.1 usr/share/man/man1/show-coords.1
 usr/share/man/man1/mummer.1 usr/share/man/man1/show-snps.1
 usr/share/man/man1/mummer.1 usr/share/man/man1/show-tiling.1
+usr/share/man/man1/delta2blocks.1 usr/share/man/man1/delta2man.1

Modified: trunk/packages/mummer/trunk/debian/mummer.manpages
===================================================================
--- trunk/packages/mummer/trunk/debian/mummer.manpages	2015-04-14 06:34:01 UTC (rev 19043)
+++ trunk/packages/mummer/trunk/debian/mummer.manpages	2015-04-14 07:34:14 UTC (rev 19044)
@@ -1 +1 @@
-debian/mummer.1
+debian/*.1