gatk3的最后一个经典版本3.8

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
licensing	Remove old licensing	2012-04-25 12:23:08 -04:00
protected/java/src/org/broadinstitute/sting	build system overhaul	2012-05-17 15:16:29 -04:00
public	Refactor on how RR treats soft clips	2012-06-21 14:02:03 -04:00
settings	Testing of BCF codec	2012-05-24 10:57:01 -04:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
build.xml	ant fasttest: for when you just can't wait	2012-06-01 15:17:18 -04:00
ivy.xml	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00