gatk3的最后一个经典版本3.8

David Roazen a96ed385df ReadShard.getReadsSpan(): handle case where shard contains only unmapped mates ... Nasty, nasty bug -- if we were extremely unlucky with shard boundaries, we might end up with a shard containing only unmapped mates of mapped reads. In this case, ReadShard.getReadsSpan() would not behave correctly, since the shard as a whole would be marked "mapped" (since it refers to mapped intervals) yet consist only of unmapped mates of mapped reads located within those intervals.		2012-10-02 13:50:00 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	Added an argument to RR to allow polyploid consensus creation (by default it is turned off). This will eventually be replaced by the known SNPs track trigger.	2012-09-28 11:44:25 -04:00
public	ReadShard.getReadsSpan(): handle case where shard contains only unmapped mates	2012-10-02 13:50:00 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00
.gitignore	a few more useful git ignores	2012-09-01 11:08:36 -04:00
build.xml	Proper error handling in NanoScheduler	2012-09-19 17:03:13 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00