David Roazen 5baf906c28 Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists ... -The algorithm for finding the intersection of two sets of intervals relies on the sortedness of the intervals within each set, but the engine was not sorting the intervals before attempting to find the intersection. -The result was that if one or both interval lists was unsorted / lexicographically sorted, we would often fail to find the intersection correctly. -Now the IntervalBinding sorts all sets of intervals before returning them, solving the problem. -Added an integration test for this case. GSA-909 #resolve		2013-04-02 14:01:52 -04:00
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R	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -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	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists	2013-04-02 14:01:52 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -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	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00