gatk3的最后一个经典版本3.8

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Guillermo del Angel 9dd109b79a Last feature request from Reich/Paavo labs: the allSitePLs feature in UG worked but not quite filled requirements. What's needed is the ability to have all 10 PLs for EVERY site, regardless of whether they are variant or not. Previous version only emitted the 10 PLs in reference sites. Problem is that, if all PLs are emitted in all sites and every single site is quad-allelic (only way to have the PLs printed out in a valid way) then the ability to filter variants and to use the INFO fields may be compromised. So, compromise solution is to go back to having biallelic PLs but emit a new FORMAT field, called APL, which has the 10 values, but all other statistics and regular PLs are computed as before. Note that integration test had to be disabled, as the BCF2 codec apparently doesn't support writing into genotype fields other than PL,DP,AD,GQ,FT and GT.		2013-07-18 12:54:52 -04:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Last feature request from Reich/Paavo labs: the allSitePLs feature in UG worked but not quite filled requirements. What's needed is the ability to have all 10 PLs for EVERY site, regardless of whether they are variant or not. Previous version only emitted the 10 PLs in reference sites. Problem is that, if all PLs are emitted in all sites and every single site is quad-allelic (only way to have the PLs printed out in a valid way) then the ability to filter variants and to use the INFO fields may be compromised.	2013-07-18 12:54:52 -04:00
public	SAMReaderID: fix bug with hash code and equals() method	2013-07-15 13:57:00 -04:00
settings	Rev picard, sam-jdk, tribble, and variant to version 1.91.1453	2013-05-07 14:21:15 -04:00
.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	Fail gracefully in the packaging system when bcel is not installed	2013-07-02 15:50:51 -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

README.md

The Genome Analysis Toolkit

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