2 Commits (ee7d85c6e608fc58ede79f08f7dbc8de9ebd3019)

Author	SHA1	Message	Date
David Roazen	03e5184741	Fix serious engine bug that could cause reads to be dropped under certain circumstances ... 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.	2012-02-13 16:25:21 -05:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, ... removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00