Mark DePristo 7f166c3198 Bugfix to compareTo and equals in GenomeLoc ... -- Yes, GenomeLoc.compareTo was broken. The compareTo function only considered the contig and start position, but not the stop, when comparing genome locs. -- Updated GenomeLoc.compareTo function to account for stop. Updated GATK code where necessary to fix resulting problems that depended on this. -- Added unit tests to ensure that hashcode, equals, and compareTo are all correct for GenomeLocs		2012-08-30 15:07:02 -04:00
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R	Actually load the library necessary to compactPDF	2012-08-28 08:06:47 -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	Bugfix to compareTo and equals in GenomeLoc	2012-08-30 15:07:02 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -04:00
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	One less Queue command line requirement: -tempDir now defaults to .queue/tmp.	2012-08-27 12:04:50 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00