gatk3的最后一个经典版本3.8

Eric Banks 562f2406d7 Added check that BaseRecalibrator is not being run on a reduced bam. ... - Throws user exception if it is. - Can be turned off with --allow_bqsr_on_reduced_bams_despite_repeated_warnings argument. - Added test to check this is working. - Added docs to BQSRReadTransformer explaining why this check is not performed on PrintReads end. - Added small bug fix to GenomeAnalysisEngine that I uncovered in this process. - Added comment about not changing the program record name, as per reviewer comments. - Removed unused variable.		2013-02-06 10:14:27 -05:00
licensing	Refrain from pushing symlinks into the repo... not all filesystems treat it correctly	2013-01-22 15:18:19 -07:00
protected/java	Added check that BaseRecalibrator is not being run on a reduced bam.	2013-02-06 10:14:27 -05:00
public	Added check that BaseRecalibrator is not being run on a reduced bam.	2013-02-06 10:14:27 -05:00
settings	Rev picard, sam-jdk, and tribble	2013-02-01 13:51:30 -05:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Move AWS keys to a resources subdirectory within the phonehome package	2013-01-31 11:56:34 -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	ReadBackedPileup cleanup	2013-01-11 15:17:18 -05:00