Mark DePristo ce3d1f89ea ReadShard are no longer allowed to span multiple contigs ... -- Previous behavior was unnecessary and causes all sorts of problems with RODs for reads. The old implementation simply failed in this case. The new code handles this correctly by forcing shards to have all of their data on a single contig. -- Added a PrintReads integration test to ensure this behavior is correct -- Adding test BAMs that have < 200 reads and span across contig boundaries		2012-08-30 10:15:11 -04:00
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commandline	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
gatk	ReadShard are no longer allowed to span multiple contigs	2012-08-30 10:15:11 -04:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	RecalDatums now hold doubles so the test for equality needs an epsilon.	2012-08-28 16:00:52 -04:00
BaseTest.java	Extensive unit tests, contacts, and documentation for RecalDatum	2012-07-31 08:11:03 -04:00
MD5DB.java	Finalizing BCF2 mark III commit	2012-06-21 15:16:27 -04:00
MD5Mismatch.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	On the way to really sorting out HMS error handling	2012-07-25 22:11:10 -04:00