As discussed in #1063, there's an existing tool, maf_stream that can squish together duplication rows in the MAF, without losing any coverage.
This was an issue that just came up for me when looking at another alignment : multiple copies not allowed, but filtering them out visibly tanks coverage.
The solution here kind of cheats in that the rows in the consensus MAF don't actually correspond the the fasta. But PhastCons only considers the columns, so that should be okay.
The interface for this is cactus-hal2maf --dupeMode consensus.
As discussed in #1063, there's an existing tool,
maf_streamthat can squish together duplication rows in the MAF, without losing any coverage.This was an issue that just came up for me when looking at another alignment : multiple copies not allowed, but filtering them out visibly tanks coverage.
The solution here kind of cheats in that the rows in the consensus MAF don't actually correspond the the fasta. But PhastCons only considers the columns, so that should be okay.
The interface for this is
cactus-hal2maf --dupeMode consensus.Resolves #1063