gatk3的最后一个经典版本3.8

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Eric Banks 64d5bf650e Pulled out some hard-coded values from the read-threading and isActive code of the HC, and made them into a single argument. In unifying the arguments it was clear that the values were inconsistent throughout the code, so now there's a single value that is intended to be more liberal in what it allows in (in an attempt to increase sensitivity). Very little code actually changes here, but just about every md5 in the HC integration tests are different (as expected). Added another integration test for the new argument. To be used by David R to test his per-branch QC framework: does this commit make the HC look better against the KB?		2014-01-19 01:15:13 -05:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Pulled out some hard-coded values from the read-threading and isActive code of the HC, and made them into a single argument.	2014-01-19 01:15:13 -05:00
public	Added an info log containing the SAM/BAM files that were eventually found from the commandline (useful for when there are files hiding inside bam.lists which may or may not have been constructed correctly...)	2014-01-17 11:25:21 -05:00
settings	Assorted fixes and improvements to gatkdocs	2014-01-13 17:46:22 -05:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
README.md	Update README file for the 2.6 release	2013-06-20 13:08:29 -04:00
build.xml	Separate tests that access the knowledge base from other tests	2013-12-06 11:31:35 -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	Changing from scala 2.9.2 to 2.10.2.	2013-09-23 12:42:22 -04:00

README.md

The Genome Analysis Toolkit

See http://www.broadinstitute.org/gatk/