gatk3的最后一个经典版本3.8

Mauricio Carneiro d16cb68539 Updated and more thorough version of the BadCigar read filter ... * No reads with Hard/Soft clips in the middle of the cigar * No reads starting with deletions (with or without preceding clips) * No reads ending in deletions (with or without follow-up clips) * No reads that are fully hard or soft clipped * No reads that have consecutive indels in the cigar (II, DD, ID or DI) Also added systematic test for good cigars and iterative test for bad cigars.		2012-08-17 17:05:27 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	FindBugs 'Efficiency' fixes	2012-08-16 15:40:52 -04:00
public	Updated and more thorough version of the BadCigar read filter	2012-08-17 17:05:27 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -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	Convert external.build.dir and external.dist.dir back to paths	2012-08-15 23:04:10 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00