Mauricio Carneiro ab53220635 Refactor on how RR treats soft clips ... * Sites with more soft clipped bases than regular will force-trigger a variant region * No more unclipping/reclipping, RR machinery now handles soft clips natively. * implemented support for base insertion and base deletion quality scores in synthetic and regular reads. * GATKSAMRecord clone() now creates a fresh object for temporary attributes if one is present. note: SAMRecords create a shallow copy of the tempAttribute object which was causing multiple reads (that came from the same read) to have their temporary attributes modified by one another inside reduce reads. Beware, if you're not using GATKSAMRecord!		2012-06-21 14:02:03 -04:00
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alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Nearing final BCF commit	2012-06-14 16:42:32 -04:00
gatk	Once I was playing with integration tests it was simple to fix the ones I left broken from earlier today.	2012-06-18 21:54:58 -04:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	Refactor on how RR treats soft clips	2012-06-21 14:02:03 -04:00
BaseTest.java	Fix bug in incorrectly reporting relative paths in log	2012-06-14 16:42:37 -04:00
MD5DB.java	Algorithmically faster version of DiffEngine	2012-06-14 16:42:30 -04:00
MD5Mismatch.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Initial version of clean, fast formatting routines built dynamically from a VCF header	2012-06-14 16:42:30 -04:00