gatk3的最后一个经典版本3.8

Eric Banks d242f1bba3 Secondary alignments were not handled correctly in IndelRealigner ... * This is emerging now because BWA-MEM produces lots of reads that are not primary alignments * The ConstrainedMateFixingManager class used by IndelRealigner was mis-adjusting SAM flags because it was getting confused by these secondary alignments * Added unit test to cover this case		2013-05-06 19:09:10 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Secondary alignments were not handled correctly in IndelRealigner	2013-05-06 19:09:10 -04:00
public	Merge pull request #208 from broadinstitute/yf_fix_molten_GenotypeConcordance	2013-05-06 08:42:06 -07:00
settings	Rev'd up Picard to get PL fix: PLs were saturated to 32767 (Short.MAX_VALUE) when converting from GL to integers. Increase capping to Integer.MAX_VALUE (2^31-1) which should be enough for reasonable sites now. Integration tests change because some tests have some hyper-deep pileups where this case was hit	2013-05-02 16:31:43 -04:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
build.xml	Include cofoja jar in classpath when testing release jars	2013-04-30 22:16:58 -04:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
ivy.xml	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00