gatk3的最后一个经典版本3.8

Eric Banks 75543a3f22 ReadClipper.clipRead's claim that it doesn't modify the original read was false. Ultimately, GATKSAMRecord.clone (as documented) creates a soft copy of the read - so modifying e.g. the bases of the cloned read means that you modify the bases of the original read too. Because of this, when the BQSRv2 Context covariate was writing Ns over the low quality tails of the reads they got propagated out to the output BAM file (very bad). I've updated the ReadClipper docs and cleaned up the code (no reason to use a clone of the read anymore given that we are already modifying the original). For now, the simplest thing is to have the Context covariate store the original bases, overwrite low quality Ns, compute covariates, and rewrite the original bases; we can update later if needed.		2012-07-13 18:50:27 -04:00
licensing	Remove old licensing	2012-04-25 12:23:08 -04:00
protected/java	Updating default value for -mindel to the one used by Khalid in the pipeline and me in my tests.	2012-07-10 02:04:26 -04:00
public	ReadClipper.clipRead's claim that it doesn't modify the original read was false. Ultimately, GATKSAMRecord.clone (as documented) creates a soft copy of the read - so modifying e.g. the bases of the cloned read means that you modify the bases of the original read too. Because of this, when the BQSRv2 Context covariate was writing Ns over the low quality tails of the reads they got propagated out to the output BAM file (very bad). I've updated the ReadClipper docs and cleaned up the code (no reason to use a clone of the read anymore given that we are already modifying the original). For now, the simplest thing is to have the Context covariate store the original bases, overwrite low quality Ns, compute covariates, and rewrite the original bases; we can update later if needed.	2012-07-13 18:50:27 -04:00
settings	Rev tribble to 110. Log is:	2012-06-26 15:28:32 -04:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
build.xml	ant fasttest: for when you just can't wait	2012-06-01 15:17:18 -04:00
ivy.xml	Navel -> GXDB	2012-06-28 13:38:00 -04:00