gatk3的最后一个经典版本3.8

Khalid Shakir 9801dd114f Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped ... The GATK -L unmapped is for GenomeLocs with SAMRecord.NO_ALIGNMENT_REFERENCE_NAME, not SAMRecord.getReadUnmappedFlag() Previously unmapped flag reads in the last bin were being printed while also seeking for the reads without a reference contig.		2012-04-27 09:58:38 -04:00
licensing	Remove old licensing	2012-04-25 12:23:08 -04:00
public	Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped	2012-04-27 09:58:38 -04:00
settings	Rev. tribble to fix BED codec bug in tribble 51	2012-01-17 16:40:26 -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
build.xml	Added function to get bases from the current base forward in the window in ReferenceContext	2012-04-06 16:07:46 -04:00
ivy.xml	S3 upload now directly creates the XML report in memory and puts that in S3	2012-01-29 15:14:58 -05:00