.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH DELTA-FILTER "1" "April 2015" "mummer 3.23" "User Commands"
.SH NAME
delta-filter \- read a delta alignment file from either nucmer or promer and filters the alignments
.SH SYNOPSIS
.B delta\-filter 
.RI [options]  <deltafile>
.SH DESCRIPTION
.TP
.BR \fB\-1\fR
1\-to\-1 alignment allowing for rearrangements (intersection of \fB\-r\fR and \fB\-q\fR alignments)
.TP
\fB\-g\fR
1\-to\-1 global alignment not allowing rearrangements
.TP
\fB\-h\fR
Display help information
.TP
\fB\-i\fR float
Set the minimum alignment identity [0, 100], default 0
.TP
\fB\-l\fR int
Set the minimum alignment length, default 0
.TP
\fB\-m\fR
Many\-to\-many alignment allowing for rearrangements (union of \fB\-r\fR and \fB\-q\fR alignments)
.TP
\fB\-q\fR
Maps each position of each query to its best hit in
the reference, allowing for reference overlaps
.TP
\fB\-r\fR
Maps each position of each reference to its best hit
in the query, allowing for query overlaps
.TP
\fB\-u\fR float      Set the minimum alignment uniqueness, i.e. percent of
.IP
the alignment matching to unique reference AND query
sequence [0, 100], default 0
.TP
\fB\-o\fR float
Set the maximum alignment overlap for \fB\-r\fR and \fB\-q\fR options
as a percent of the alignment length [0, 100], default 100
.TP
\fB\-v\fR
Print the discarded alignments instead of those that pass filters
.TP
\fB\-b\fR
Maps duplications
(XOR of \fB\-r\fR and \fB\-q\fR alignments, one or the other but not both)
.PP
Reads a delta alignment file from either nucmer or promer and
filters the alignments based on the command\-line switches, leaving
only the desired alignments which are output to stdout in the same
delta format as the input. For multiple switches, order of operations
is as follows: \fB\-i\fR \fB\-l\fR \fB\-u\fR \fB\-q\fR \fB\-r\fR \fB\-g\fR \fB\-m\fR \fB\-1\fR \fB\-b\fR. If an alignment is excluded
by a preceding operation, it will be ignored by the succeeding
operations.
.PP
An important distinction between the \fB\-g\fR option and the \fB\-1\fR and \fB\-m\fR
options is that \fB\-g\fR requires the alignments to be mutually consistent
in their order, while the \fB\-1\fR and \fB\-m\fR options are not required to be
mutually consistent and therefore tolerate translocations,
inversions, etc. In general cases, the \fB\-m\fR option is the best choice,
however \fB\-1\fR can be handy for applications such as SNP finding which
require a 1\-to\-1 mapping. Finally, for mapping query contigs, or
sequencing reads, to a reference genome, use \fB\-q\fR. The duplications
printed with the \fB\-b\fR option are \fB\-r\fR and \fB\-q\fR alignments that are not
present in the 1\-to\-1 alignment. These alignments are also the
difference between the \fB\-1\fR and \fB\-m\fR alignments
.SH SEE ALSO
The \fB\-b\fR option 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