gatk3的最后一个经典版本3.8

Eric Banks 27d8d3f51e RR optimization: don't recalculate the entire bitset of variant sites for every read added to the sliding window. Instead, reuse as much of the previously calculated bitset as you can (basically from the window start until the start of the new read minus the context size). In some awfully performing regions this cuts down the runtime in half, although in others this doesn't seem to help much (so clearly something else is going on). Note that I still need to fix one last bug here, but it's almost done.		2012-10-19 11:59:34 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	RR optimization: don't recalculate the entire bitset of variant sites for every read added to the sliding window. Instead, reuse as much of the previously calculated bitset as you can (basically from the window start until the start of the new read minus the context size). In some awfully performing regions this cuts down the runtime in half, although in others this doesn't seem to help much (so clearly something else is going on). Note that I still need to fix one last bug here, but it's almost done.	2012-10-19 11:59:34 -04:00
public	Better implementation for getSoftEnd() in GATKSAMRecord	2012-10-18 09:01:51 -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