bigdatagenomics/bdg-formats — pull request #21 by fnothaft (2014-07-13 10:52:06+00:00)
Title: Changing read to alignment record.

See #19.

AlignmentRecord is a preferable choice vs. Read, because a single read can have multiple alignments, thus a Read structure won't preserve the 1:1 mapping that it implies. For unaligned reads, an AlignmentRecord will just note that it is unaligned.