gatk3的最后一个经典版本3.8

aaron b6874f30cb Added changes to bounded read iterator, it now explicitly takes a MSRI2 instead of the interfaces ClosableIterator<SAMRecord>. It would be good to fix this in the future with an interface that lets you get the (possibly merged) header. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@552 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-28 17:57:54 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	Updated the hello world document to reflect system changes.	2009-04-22 23:25:15 +00:00
java	Added changes to bounded read iterator, it now explicitly takes a MSRI2 instead of the interfaces ClosableIterator<SAMRecord>. It would be good to fix this in the future with an interface that lets you get the (possibly merged) header.	2009-04-28 17:57:54 +00:00
python	Several changes to CovariateCounter walker to print more tables (called vs. observed Q scores), bug fixes to LogisticRecalibrationWalker and LogisticRegressor, and print string functionality added to Pair.	2009-04-28 00:37:48 +00:00
settings	Revert accidental checkin of hacked picard build.	2009-04-27 09:47:10 +00:00
shell	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
testdata	Basic logistic regression support for calibrating qualities; mostly for Andrew to experiment with	2009-04-24 19:09:50 +00:00
build.xml	Added the base test case, fixed the rest of the test cases to follow suit. Added more verbose output to ant for junit tests.	2009-04-14 17:11:38 +00:00
ivy.xml	Added castor dependency.	2009-04-07 22:27:39 +00:00