gatk3的最后一个经典版本3.8

Ami Levy Moonshine ef3882f439 PhaseByTransmission: small typo /n. variantCallQC_summaryTablesOnly.R: small changes (more to come) /n GeneralCallingPipeline.scala: the new pipeline script. It is not as clean as I want it to be, but it works. I still going to work on it a little bit more. Also, it does not include yet: (1) the RR step (2) need better eval step (3) need to include other targets (currently it eork on the CEU Trio)		2012-10-11 14:51:41 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	Added an argument to RR to allow polyploid consensus creation (by default it is turned off). This will eventually be replaced by the known SNPs track trigger.	2012-09-28 11:44:25 -04:00
public	PhaseByTransmission: small typo /n. variantCallQC_summaryTablesOnly.R: small changes (more to come) /n GeneralCallingPipeline.scala: the new pipeline script. It is not as clean as I want it to be, but it works. I still going to work on it a little bit more. Also, it does not include yet: (1) the RR step (2) need better eval step (3) need to include other targets (currently it eork on the CEU Trio)	2012-10-11 14:51:41 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00
.gitignore	a few more useful git ignores	2012-09-01 11:08:36 -04:00
build.xml	Proper error handling in NanoScheduler	2012-09-19 17:03:13 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00