genome/breakdancer — pull request #3 by bpow (2013-02-04 03:12:29+00:00)
Title: allow for readgroup IDs to be unique by file (rather than unique overall...)

breakdancer keeps maps of readgroup->library and readgroup->platform, but assumes that readgroup ids are unique even between files (instead of just being unique within a file). This causes problems if two different files have different libraries/samples with the same readgroup id. These changes make the readgroup_library and readgroup_platform maps into multimaps first accessed by the bamfile, then by readgroup.