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
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R	Protect ourselves when iteration is present but there's only a single iteration in queueJobReport.R	2011-12-19 10:08:38 -05:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Fix serious engine bug that could cause reads to be dropped under certain circumstances	2012-02-13 16:25:21 -05:00
packages	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	When an interval list specifies overlapping intervals merge them before scattering.	2012-02-08 02:12:16 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00