9f5f6f9bc7
N-way parallelism. Works for small test cases. Untested for large test cases.
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-Needs more comprehensive unit testing.
-Needs some basic refactoring.
-Needs rethink of interface boundaries.
-Needs to play more nicely in the /tmp sandbox.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@583 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 19:34:09 +00:00
63403d32cd
Changes to the interface to the simple data source rippled out to a bunch of files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@572 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 20:35:56 +00:00
19e4e97f21
Add tag to ignore node class.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@571 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 20:27:34 +00:00
7f173af2ea
Encapsulate output tracking a bit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@570 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 15:12:13 +00:00
95d10ba314
Sketch of hierarchical reduce process, with unit tests for some core classes. Requires breakout of inner classes, testing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@565 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 20:26:16 +00:00
6b02248298
moved the test cases out of the GenomeAnalysisTK code and into a JUnit test case
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@555 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 21:49:17 +00:00
0720d248ce
Adding the test case for by reads sharding of BAM data sources
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@509 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 18:01:22 +00:00
180ff13290
Added a bunch of changes to support the new MicroManager code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@431 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 18:29:38 +00:00
6db9127f90
Added changes to shattering, refactored SAMBAM into SAM
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@426 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 13:52:56 +00:00
e6fb122d7d
Added some fixes and new iterator tests
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--This lin e, and those below, will be ignored--
A gatk/iterators
AM gatk/iterators/BoundedReadIteratorTest.java
M gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@420 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:19:36 +00:00
96248cdec4
Added some output to all the classes, including build in runtime analysis
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@411 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 19:14:53 +00:00
0629f79049
Moved fasta support files into their own package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@408 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 18:13:23 +00:00
88ebf1a05b
Fied some documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@406 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:41:38 +00:00
4b3578e1de
Added the base test case, fixed the rest of the test cases to follow suit. Added more verbose output to ant for junit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@403 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:11:38 +00:00
eb4b4a053b
A bunch of updates to the SAM/BAM data source, along with test cases for the merging of multiple files (it works!).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@399 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 14:19:20 +00:00
887adcfc7f
Some minor fixes to the last check-in
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@387 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 18:24:51 +00:00
9afa101465
Add interval support to the
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.__ __ __
_____| |__ _____ _/ |__/ |_ ___________
/ ___/ | \\__ \\ __\ __\/ __ \_ __ \
\___ \| Y \/ __ \| | | | \ ___/| | \/
/____ >___| (____ /__| |__| \___ >__|
\/ \/ \/ \/
classes!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@352 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 21:23:43 +00:00
8e2f5471a1
Some cleanup to the data source, and another JUnit test case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@344 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 14:58:05 +00:00
d517245beb
Fixes for shattering, added JUnit test case
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@332 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 16:37:34 +00:00
hanna
aaron