Eric Banks 9c0207f8ef Fixing BQSR/BAQ bug: ... If a read had an existing BAQ tag, was clipped by our engine, and couldn't have the BAQ recalculated (for whatever reason), then we would fail in the BQSR because we would default to using the old tag (which no longer matched the length of the read bases). The right thing to do here is to remove the old BAQ tag when RECALCULATE and ADD_TAG are the BAQ modes used but BAQ cannot be recalculated. Added a unit test to ensure that the tags are removed in such a case.		2013-01-31 11:03:17 -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	Fixing BQSR/BAQ bug:	2013-01-31 11:03:17 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Remove the ability to package GATK/Queue Lite from the build system	2013-01-28 02:42:37 -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