gatk3的最后一个经典版本3.8

Mauricio Carneiro cadff40247 getRefCoordSoftUnclippedStart and End refactor ... These functions are methods of the read, and supplement getAlignmentStart() and getUnclippedStart() by calculating the unclipped start counting only soft clips. * Removed from ReadUtils * Added to GATKSAMRecord * Changed name to getSoftStart() and getSoftEnd * Updated third party code accordingly.		2011-12-20 17:48:51 -05:00
public	getRefCoordSoftUnclippedStart and End refactor	2011-12-20 17:48:51 -05:00
settings	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
LICENSE	One last test...	2011-06-28 19:18:17 -04:00
build.xml	Extensive unit test for GenotypeContextUnitTest	2011-11-20 18:28:01 -05:00
ivy.xml	Updating the HybridSelectionPipeline for SnpEff 2.0.4 RC3	2011-11-17 14:46:12 -05:00