gatk3的最后一个经典版本3.8

Mark DePristo 0f0188ddb1 Optimization of BQSR ... -- Created a ReadRecalibrationInfo class that holds all of the information (read, base quality vectors, error vectors) for a read for the call to updateDataForRead in RecalibrationEngine. This object has a restrictive interface to just get information about specific qual and error values at offset and for event type. This restrict allows us to avoid creating an vector of byte 45 for each read to represent BI and BD values not in the reads. Shaves 5% of the runtime off the entire code. -- Cleaned up code and added lots more docs -- With this commit we no longer have much in the way of low-hanging fruit left in the optimization of BQSR. 95% of the runtime is spent in BAQing the read, and updating the RecalData in the NestedIntegerArrays.		2012-12-24 13:35:09 -05:00
licensing	Final final final version of the license.	2012-07-20 18:00:02 -04:00
protected/java	Optimization of BQSR	2012-12-24 13:35:09 -05:00
public	Optimization of BQSR	2012-12-24 13:35:09 -05:00
settings	Final r119 tribble jar	2012-11-02 14:30:33 -04:00
.gitignore	adding some directories to gitignore	2012-09-27 11:09:41 -04:00
build.xml	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -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	Use build jars in test classpaths by default	2012-11-28 22:57:04 -05:00