Convert axt format to raf format.

axt2raf.py: convert axt format to raf format

The axt format is used to describe the segments of one genome that align to another. For example, there are axt files that describe the alignment of the chimpanzee reference sequence to human one. Given such a file, axt2raf.py will generate a .raf file that maps the bases of the chimpanzee sequence onto human coordinates. Because reference genomes are haploid, the output .raf file will have only 0s and 1s as reference allele frequencies.

usage: axt2raf.py [options] [inputfile]
where options may include:

   -minlen <x>  : set min alignment length to <x> base pairs
   -minqual <x> : set min alignment quality to <x>

Program reads from "inputfile" if provided, or otherwise from
standard input. Input should be in axt format.

Writes to standard output.