maf2anchors -- Converts maf files into Murasaki anchor sets
- --prefix=<S>
- use <S> as a prefix for output file names (otherwise uses
<file.maf>)
- --rifts=<I>
- allow up to <I> rifts.
- --fakeseqs
- generate fake sequence length files and sequence stubs based on sequence
length data in MAF file
- --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).
- --sort
- Sort the sequences found by --trust (so as to match the output that would
have happened with --notrust).