Mauricio Carneiro d16cb68539 Updated and more thorough version of the BadCigar read filter ... * No reads with Hard/Soft clips in the middle of the cigar * No reads starting with deletions (with or without preceding clips) * No reads ending in deletions (with or without follow-up clips) * No reads that are fully hard or soft clipped * No reads that have consecutive indels in the cigar (II, DD, ID or DI) Also added systematic test for good cigars and iterative test for bad cigars.		2012-08-17 17:05:27 -04:00
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R	Fix for missing formatter in R 2.15	2012-08-17 11:49:02 -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	Updated and more thorough version of the BadCigar read filter	2012-08-17 17:05:27 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Bugfix for potential SEGFAULT with JNA getting execution hosts for LSF with multiple hosts	2012-08-17 11:49:01 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00