gatk3的最后一个经典版本3.8

Mauricio Carneiro 4aad7e23ef New ReduceReads v2 with unclipped variant regions and soft-clipped bases ... * Re-wrote the sliding window approach to allow the variant region not to clip the reads that overlap it. * Updated consensus to include only reads that were not passed on by the variant region, header counts are updated on the fly to avoid recompute * Added soft clipped bases to ReduceReads analysis by unclipping high quality soft-clips then re-clipping after reduce reads * Updated all integration tests		2012-06-08 14:58:31 -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	New ReduceReads v2 with unclipped variant regions and soft-clipped bases	2012-06-08 14:58:31 -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