gatk3的最后一个经典版本3.8

David Roazen c4b0ba4d45 Temporarily back out the Picard team's patches to GATKBAMIndex from December ... These patches to GATKBAMIndex are causing massive BAM index reading errors in combination with the latest version of Picard. The bug is either in the patches themselves or in the underlying SeekableBufferedStream class they rely on. Until the cause can be identified, we are temporarily backing out these changes so that we can continue to run with the latest Picard/Tribble. This reverts commits: 81483ec21e528790dfa719d18cdee27d577ca98e 68cf0309db490b79eecdabb4034987ff825ffea8 54bb68f28ad5fe1b3df01702e9c5e108106a0176		2013-02-01 13:51:31 -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	Add option to specify maximum STR length to RepeatCovariates from command line to ease testing	2013-02-01 13:51:31 -05:00
public	Temporarily back out the Picard team's patches to GATKBAMIndex from December	2013-02-01 13:51:31 -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