When aggregating raw BAM file spans into shards, the IntervalSharder tries to combine
file spans when it can. Unfortunately, the method that combines two BAM file
spans was seriously flawed, and would produce a truncated union if the file spans
overlapped in certain ways. This could cause entire regions of the BAM file containing
reads within the requested intervals to be dropped.
Modified GATKBAMFileSpan.union() to correct this problem, and added unit tests
to verify that the correct union is produced regardless of how the file spans
happen to overlap.
Thanks to Khalid, who did at least as much work on this bug as I did.
This change and my previous change have dropped runtime when dynamically merging 2k BAM files from 72.6min/1M reads to 46.8sec/1M reads.
Note that many of these changes are stopgaps -- the real problem is the way ReadWalkers interface with Picard, and I'll have to work with
Tim&Co to produce a more maintainable patch.
David Roazen
Matt Hanna
Mark DePristo