maf-convert.py
==============

This script reads alignments in maf format, and writes them in another
format.  It can write them in these formats: axt, blast, html, psl,
sam, tab.  You can use it like this:

  maf-convert.py psl my-alignments.maf > my-alignments.psl

The input should be "multiple alignment format" as described in the
UCSC Genome FAQ (not "MIRA assembly format" or any other maf).

For html: if the input includes probability lines starting with 'p',
then the output will be coloured by column probability.  (To get lines
starting with 'p', run lastal with option -j4 or -j5.)  If an
alignment has multiple 'p' lines (e.g. after using maf-join.py), then
the column-wise products are used.

Options
-------

  -h, --help
         Print a help message and exit.

  -p, --protein
         Specify that the alignments are of proteins, rather than
         nucleotides.  This affects psl format only (the first 4
         columns).

  -d, --dictionary
         Include a dictionary of sequence lengths in the sam header
         section.  This requires reading the input twice, so it must
         be a real file (not a pipe).  This affects sam format only.

  -l CHARS, --linesize=CHARS
         Write CHARS characters per line.  This affects blast and html
         formats only.

"Bugs"
------

* For sam: the QUAL field (column 11) is simply copied from the maf q
  line.  The QUAL is supposed to be encoded as ASCII(phred+33),
  whereas maf q lines are encoded differently according to the UCSC
  Genome FAQ.  However, if you run lastal with option -Q1, the maf q
  lines will in fact be ASCII(phred+33).

* The blast format is merely blast-like: it is not identical to NCBI
  BLAST.
