Yossi Farjoun 3a7c8c13e2 Re-enabled fastBAMindexing by replacing the FileChannel with a SeekableBufferedStream ... This helps a lot since FileChannel is very low-level and traversing the BAMIndex involves lots of short reads. - Fixed a deterioration in BAMIndex due to rev'ed picard (see below) - Added unit tests for SeekableBufferedStream - Added integrationTests for GATKBAMIndex (in PileupWalkerIntegrationTest) - Added a runtime-test to verify that the amount read equals the amount requested. - Added failing tests with expectedExceptions - Used a DataProvider to make code nicer		2013-02-14 17:51:15 -05:00
..
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
chainFiles	…
doc	…
java	Re-enabled fastBAMindexing by replacing the FileChannel with a SeekableBufferedStream	2013-02-14 17:51:15 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Rev picard, sam-jdk, and tribble	2013-02-01 13:51:30 -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	Message "script failed" moved to the correct place in the code	2013-02-04 15:37:23 -05:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00