gatk3的最后一个经典版本3.8

Mark DePristo 61f0c46423 Rev tribble to 110. Log is: ... Optimization for PositionalBufferedStream with specialized read(byte, int, int) method -- For binary codecs having an efficient reader of lots of bytes that doesn't fall back into read() itself vastly improves performance. The old version was 10x slower than InputStream, while the new version is +30%. -- Generalize PositionalBufferedStream main() method for performance testing, now accepts cmdline arguments for the file to read, how many iterations, etc Generalize AsciiLineReader main() method for performance testing -- Now accepts cmdline arguments for the file to read, how many iterations, etc AsciiLineReaderTest and PositionBufferedStreamTest were in src not test/src		2012-06-26 15:28:32 -04:00
licensing	Remove old licensing	2012-04-25 12:23:08 -04:00
protected/java	Moving ReduceReads into protected	2012-06-25 17:01:33 -04:00
public	Bugfix for shadow BCFs to not attempt to write to /dev/null.bcf	2012-06-26 15:28:32 -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	JEXL update	2012-06-21 15:17:21 -04:00