gatk-3.8

Author	SHA1	Message	Date
aaron	de6ae51f7e	Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar. A couple of notes: -Commented out BaseTransitionTableCalculator.scala because it's won't build; Chris could you fix this one (or kill it if it's not needed). -Removed the PrintReadsScala walker; moved the code over to a ScalaCountLoci walker (which is what the code was really doing). -Added configurations items to the ivy xml file. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1956 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-02 06:02:41 +00:00
hanna	b43925c01e	Switched to Reflections (http://code.google.com/p/reflections/) project for inspecting the source tree and loading walkers, rather than trying to roll our own by hand. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1286 348d0f76-0448-11de-a6fe-93d51630548a	2009-07-21 18:32:22 +00:00
kiran	0a0ef573f7	Methods for finding classes given a path and finding classes that implement a given interface. This stuff was mostly copied from private methods in WalkerManager, so there's some code redundancy. At some point, those calls could be replaced with these. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1053 348d0f76-0448-11de-a6fe-93d51630548a	2009-06-18 22:43:19 +00:00

Author

SHA1

Message

Date

aaron

Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.

A couple of notes:
-Commented out BaseTransitionTableCalculator.scala because it's won't build; Chris could you fix this one (or kill it if it's not needed).
-Removed the PrintReadsScala walker; moved the code over to a ScalaCountLoci walker (which is what the code was really doing).
-Added configurations items to the ivy xml file.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1956 348d0f76-0448-11de-a6fe-93d51630548a

2009-11-02 06:02:41 +00:00

hanna

b43925c01e

Switched to Reflections (http://code.google.com/p/reflections/) project for

inspecting the source tree and loading walkers, rather than trying to roll
our own by hand.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1286 348d0f76-0448-11de-a6fe-93d51630548a

2009-07-21 18:32:22 +00:00

kiran

0a0ef573f7

Methods for finding classes given a path and finding classes that implement a given interface. This stuff was mostly copied from private methods in WalkerManager, so there's some code redundancy. At some point, those calls could be replaced with these.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1053 348d0f76-0448-11de-a6fe-93d51630548a

2009-06-18 22:43:19 +00:00

3 Commits (de6ae51f7e382b1775be13acf227631f1467eacf)