Mark DePristo 0ac4352614 LIBS can now (optionally) track the unique reads it uses from the underlying read iterator ... -- This capability is essential to provide an ordered set of used reads to downstream users of LIBS, such as ART, who want an efficient way to get the reads used in LIBS -- Vastly expanded the multi-read, multi-sample LIBS unit tests to make sure this capability is working -- Added createReadStream to ArtificialSAMUtils that makes it relatively easy to create multi-read, multi-sample read streams for testing		2013-01-11 15:17:16 -05:00
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R	Fix a nasty bug in reading GATK reports with a single line	2012-09-10 20:14:13 -04:00
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java	LIBS can now (optionally) track the unique reads it uses from the underlying read iterator	2013-01-11 15:17:16 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Remove DepthOfCoverage.java because it is no longer public	2013-01-10 11:45:38 -05:00
perl	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	Licensing update -- batch #2	2013-01-11 13:38:11 -05:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00