gatk3的最后一个经典版本3.8

Eric Banks 58424e56be Setting the reduce reads count tag was all wrong in a previous commit; fixing. ... RR counts are represented as offsets from the first count, but that wasn't being done correctly when counts are adjusted on the fly. Also, we were triggering the expensive conversion and writing to binary tags even when we weren't going to write the read to disk. The code has been updated so that unconverted counts are passed to the GATKSAMRecord and it knows how to encode the tag correctly. Also, there are now methods to write to the reduced counts array without forcing the conversion (and methods that do force the conversion). Also: 1. counts are now maintained as ints whenever possible. Only the GATKSAMRecord knows about the internal encoding. 2. as discussed in meetings today, we updated the encoding so that it can now handle a range of values that extends to 255 instead of 127 (and is backwards compatible). 3. tests have been moved from SyntheticReadUnitTest to GATKSAMRecordUnitTest accordingly.		2013-04-30 13:45:42 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Setting the reduce reads count tag was all wrong in a previous commit; fixing.	2013-04-30 13:45:42 -04:00
public	Setting the reduce reads count tag was all wrong in a previous commit; fixing.	2013-04-30 13:45:42 -04:00
settings	Rev picard, sam-jdk, tribble, and variant jars to version 1.90.1442	2013-04-25 14:05:24 -04:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
build.xml	Add additional necessary class files to na12878kb.jar target	2013-04-23 14:03:48 -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