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gatk3的最后一个经典版本3.8
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Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
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hanna 83b8676b69 Hack to fix mysterious disappearing read attributes. Ultimately caused 
by the fact that the GATKSAMRecord, by design, needs to both inherit from 
SAMRecord and wrap a 'member' SAMRecord, and method calls that aren't
implemented as explicit passthroughs can compromise the content of the
SAMRecord in subtle ways.

Will be automatically fixed when Picard moves to a lightweight SAMRecord
interface rather than the current heavyweight implementation.  But in 
the short-term, there's no obvious fix.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4489 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-10-13 19:06:54 +00:00
R Better reporting -- figured out how to drop unused levels in subset 2010-10-06 14:31:51 +00:00
archive Cleaning up playground utils and tests 2010-08-27 01:25:47 +00:00
c Reduce file handle usage. 2010-01-05 18:03:01 +00:00
doc removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also 2010-08-19 00:42:37 +00:00
java Hack to fix mysterious disappearing read attributes. Ultimately caused 2010-10-13 19:06:54 +00:00
matlab Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function 2009-11-30 20:02:25 +00:00
packages Include all standard annotations 2010-10-11 20:52:08 +00:00
perl Adding a script to do big table conversion. Removing Ben's script which is totally obsolete and busted. 2010-10-12 01:40:43 +00:00
python Adding a script to do big table conversion. Removing Ben's script which is totally obsolete and busted. 2010-10-12 01:40:43 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Scala protected is more akin to Java private than Java protected. Not typing these defs. 2010-10-08 19:36:23 +00:00
settings Wrapping ScatterGatherableFunctions with a facade instead of using slower clone library. Will require keeping Clone's facade code in sync with CommandLineFunction but runs *much* faster. 2010-10-07 01:19:18 +00:00
shell Inprocess functions by default now log what output files they are running for. 2010-10-07 19:08:02 +00:00
testdata Fixes for example bam files 2010-10-05 18:43:02 +00:00
LICENSE Adding a license to the root directory in case BOSC checks for one. Has the 2010-04-20 16:04:29 +00:00
build.xml Wrapping ScatterGatherableFunctions with a facade instead of using slower clone library. Will require keeping Clone's facade code in sync with CommandLineFunction but runs *much* faster. 2010-10-07 01:19:18 +00:00
ivy.xml Wrapping ScatterGatherableFunctions with a facade instead of using slower clone library. Will require keeping Clone's facade code in sync with CommandLineFunction but runs *much* faster. 2010-10-07 01:19:18 +00:00