Eric Banks 6dc52d42bf Implemented the proper QUAL calculation for multi-allelic calls. Integration tests pass except for the ones making multi-allelic calls (duh) and one of the SLOD tests (which used to print 0 when one of the LODs was NaN but now we just don't print the SB annotation for that record).		2011-12-18 00:01:42 -05:00
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R	scales=free shows variance within analysis better	2011-12-07 14:09:32 -05:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	…
doc	…
java	Implemented the proper QUAL calculation for multi-allelic calls. Integration tests pass except for the ones making multi-allelic calls (duh) and one of the SLOD tests (which used to print 0 when one of the LODs was NaN but now we just don't print the SB annotation for that record).	2011-12-18 00:01:42 -05:00
packages	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Added test mode to PPP	2011-12-12 18:29:06 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00