cactus-hal2maf filters out gaps and unaligned regions automatically. I think this was originally done to better fit what the Genome Browser expects. But at least a few people have been disappointed to not find their entire reference interval in the MAF whether or not it's aligned.
So this PR takes this filter step out of cactus-hal2maf and, since it's browser-specific, moves it into cactus-maf2bigmaf
cactus-hal2maffilters out gaps and unaligned regions automatically. I think this was originally done to better fit what the Genome Browser expects. But at least a few people have been disappointed to not find their entire reference interval in the MAF whether or not it's aligned.So this PR takes this filter step out of
cactus-hal2mafand, since it's browser-specific, moves it intocactus-maf2bigmafResolves #1362