Eric Banks 6df43f730a Fixing ReadBackedPileup to represent mapping qualities as ints, not (signed) bytes. ... Having them as bytes caused problems for downstream programmers who had data with high MQs.		2013-07-23 23:47:15 -04:00
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R	Removed plots generation from the BaseRecalibration software	2013-06-19 14:47:56 -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	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Fixing ReadBackedPileup to represent mapping qualities as ints, not (signed) bytes.	2013-07-23 23:47:15 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -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	Disable RetryMemoryLimit pipeline test	2013-07-03 13:38:28 -04:00
testdata	Walker to create a fastq file from an interval list	2013-06-29 11:24:16 -04:00