Eric Banks 4e5ff3d6f1 Bug fix for NPE in HC with --dbsnp argument. ... - I had added the framework in the VA engine but should not have hooked it up to the HC yet since the RefMetaDataTracker is always null. - Added contracts and docs to the relevant methods in the VA engine so that this doesn't happen in the future.		2013-02-05 21:59:19 -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	Bug fix for NPE in HC with --dbsnp argument.	2013-02-05 21:59:19 -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