Mark DePristo aff508e091 ReadGroupProperties walker and associated infrastructure ... -- ReadGroupProperties: Emits a GATKReport containing read group, sample, library, platform, center, median insert size and median read length for each read group in every BAM file. -- Median tool that collects up to a given maximum number of elements and returns the median of the elements. -- Unit and integration tests for everything. -- Making name of TestProvider protected so subclasses and override name more easily		2012-03-01 15:01:11 -05:00
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alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	ReadGroupProperties walker and associated infrastructure	2012-03-01 15:01:11 -05:00
jna	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
utils	DNA Sequence to BitSet and vice-versa conversion tools	2012-02-29 19:25:20 -05:00
BaseTest.java	ReadGroupProperties walker and associated infrastructure	2012-03-01 15:01:11 -05:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
MedianUnitTest.java	ReadGroupProperties walker and associated infrastructure	2012-03-01 15:01:11 -05:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	All MD5 mismatches for test are shown	2011-10-04 15:53:52 -07:00