David Roazen 292037dfda Rev picard, sam-jdk, and tribble ... This is a necessary prerequisite for the org.broadinstitute.variant migration. -Picard and sam-jdk go from version 1.67.1197 to 1.84.1337 -Picard-private goes from version 2375 to 2662 -Tribble goes from version 119 to 1.84.1337 -RADICALLY trimmed down the list of classes we extract from Picard-private (jar goes from 326993 bytes to 6445 bytes!)		2013-02-01 13:51:30 -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	Rev picard, sam-jdk, and tribble	2013-02-01 13:51:30 -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	Making metrics a required parameter in MarkDuplicates	2013-01-25 17:49:49 -05:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00