Mauricio Carneiro a52e3c7e15 Revert "Bug fix for RR: don't let the softclip start position be less than 1" ... this introduced a bug in reduce reads by de-activating it's hard clipping of the out of bounds soft-clips (specially in the MT). DEV-322 #resolve #time 4m This reverts commit 42acfd9d0bccfc0411944c342a5b889f5feae736.		2012-12-12 13:09:39 -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	Revert "Bug fix for RR: don't let the softclip start position be less than 1"	2012-12-12 13:09:39 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Update GATK packaging settings to package arbitrary resources	2012-11-28 15:26:05 -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	Bringing latest performance updates from the GATK to CMI	2012-12-05 21:40:03 -05:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00