Mark DePristo 4d0e7b50ec ArtificialBAMBuilder utility class for creating streams of GATKSAMRecords with a variety of properties ... -- Allows us to make a stream of reads or an index BAM file with read having the following properties (coming from n samples, of fixed read length and aligned to the genome with M operator, having N reads per alignment start, skipping N bases between each alignment start, starting at a given alignment start) -- This stream can be handed back to the caller immediately, or written to an indexed BAM file -- Update LocusIteratorByStateUnitTest to use this functionality (which was refactored from LIBS unit tests and ArtificialSAMUtils)		2013-01-16 15:29:59 -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
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
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java	ArtificialBAMBuilder utility class for creating streams of GATKSAMRecords with a variety of properties	2013-01-16 15:29:59 -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	Re-committing the following changes from Dec 18:	2013-01-16 12:43:15 -05:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00