gatk3的最后一个经典版本3.8

Eric Banks b6839b3049 Added checking in the GATK for mis-encoded quality scores. ... The check is performed by a Read Transformer that samples (currently set to once every 1000 reads so that we don't hurt overall GATK performance) from the input reads and checks to make sure that none of the base quals is too high (> Q60). If we encounter such a base then we fail with a User Error. * Can be over-ridden with --allow_potentially_misencoded_quality_scores. * Also, the user can choose to fix his quals on the fly (presumably using PrintReads to write out a fixed bam) with the --fix_misencoded_quality_scores argument. Added unit tests.		2012-12-03 11:18:41 -05:00
licensing	Final final final version of the license.	2012-07-20 18:00:02 -04:00
protected/java	Updating md5 for UG	2012-12-01 14:24:19 -05:00
public	Added checking in the GATK for mis-encoded quality scores.	2012-12-03 11:18:41 -05:00
settings	Final r119 tribble jar	2012-11-02 14:30:33 -04:00
.gitignore	adding some directories to gitignore	2012-09-27 11:09:41 -04:00
build.xml	Refactored entire NA12878KB to allow us to easily build a na12878kb.jar for IGV integration	2012-11-29 14:38:09 -05:00
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	Use build jars in test classpaths by default	2012-11-28 22:57:04 -05:00