Ami Levy-Moonshine 2e3284f306 Continue to fix the case where PRIORITIZE is used but no priority list is given. While fixing that case I also removed unnecessary sorting, when the prioeity list is not provied. When the priority list is not provided, it will continue to be null. Thus, the number of original Variant Contexts should be given as a new parameter to simpleMerge (since priority might be null). This new parameter is used for checking if there are filtered VC, when annotationOrigin is true.		2012-12-10 22:23:58 -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
chainFiles	…
doc	…
java	Continue to fix the case where PRIORITIZE is used but no priority list is given. While fixing that case I also removed unnecessary sorting, when the prioeity list is not provied. When the priority list is not provided, it will continue to be null. Thus, the number of original Variant Contexts should be given as a new parameter to simpleMerge (since priority might be null). This new parameter is used for checking if there are filtered VC, when annotationOrigin is true.	2012-12-10 22:23:58 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Update GATK packaging settings to package arbitrary resources	2012-11-28 15:26:05 -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	Add walltime changes to LSF	2012-11-29 15:23:37 -05:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00