.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH DELTA2BLOCKS "1" "April 2015" "mummer 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),
other options include 1 (BLOSUM 45) and 3 (BLOSUM 80)
.br
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