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.IX Title "MAF2ANCHORS 1"
.TH MAF2ANCHORS 1 2024-11-09 "perl v5.40.0" "User Contributed Perl Documentation"
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.SH NAME
maf2anchors \-\- Converts maf files into Murasaki anchor sets
.SH SYNOPSIS
.IX Header "SYNOPSIS"
maf2anchors <file.maf>
.SH OPTIONS
.IX Header "OPTIONS"
.IP \-\-prefix=<S> 4
.IX Item "--prefix=<S>"
use <S> as a prefix for output file names (otherwise uses <file.maf>)
.IP \-\-rifts=<I> 4
.IX Item "--rifts=<I>"
allow up to <I> rifts.
.IP \-\-fakeseqs 4
.IX Item "--fakeseqs"
generate fake sequence length files and sequence stubs based on sequence length data in MAF file
.IP \-\-trust 4
.IX Item "--trust"
trust the comment annotation added by TBA on the second line of the
file (if present) that it lists tree used in the alignment and all of
the sequences involved. Defaults to on. use \-\-notrust to distrust TBA
tags (technically this data isn't part of the file format
specification and is just crammed into comments that TBA produces, but
might not be present or accurate on all MAF files, thus we give you
the option to distrust it).
.IP \-\-sort 4
.IX Item "--sort"
Sort the sequences found by \-\-trust (so as to match the output that would have happened
with \-\-notrust).