Eric Banks 562f2406d7 Added check that BaseRecalibrator is not being run on a reduced bam. ... - Throws user exception if it is. - Can be turned off with --allow_bqsr_on_reduced_bams_despite_repeated_warnings argument. - Added test to check this is working. - Added docs to BQSRReadTransformer explaining why this check is not performed on PrintReads end. - Added small bug fix to GenomeAnalysisEngine that I uncovered in this process. - Added comment about not changing the program record name, as per reviewer comments. - Removed unused variable.		2013-02-06 10:14:27 -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	Added check that BaseRecalibrator is not being run on a reduced bam.	2013-02-06 10:14:27 -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