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23 Commits (2a803e90444ec3becdfd3ec7b59c8a8a09056038)

Author SHA1 Message Date
ebanks 9dff578706 Added PG tag to bam header to let people know it's been cleaned. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3284 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 17:30:30 +00:00
ebanks c44f63c846 Fixing the performance tests: we need to catch the RuntimeException (not samtools' RuntimeIOExcpetion). Also, CountCovariates doesn't need the catch. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3196 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-19 14:28:12 +00:00
aaron be7cbf948b adding a catch for the exception thrown by samtools when it attempts to close /dev/null in the performance tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3186 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 17:41:48 +00:00
ebanks d06c7835d8 Adding performance tests for the indel realigner; should take ~3 hours. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3151 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-11 04:45:22 +00:00
ebanks 40d305bc7e Added test of Nway cleaning for Matt; thanks to Aaron for the help. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2977 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 21:00:41 +00:00
ebanks 0dd65461a1 Various improvements to plink, variant context, and VCF code. 
We almost completely support indels. Not yet done with plink stuff.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2926 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 17:58:01 +00:00
ebanks 8b555ff17c Killed the old cleaner code. Bye bye. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2868 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-22 20:49:58 +00:00
ebanks 79ab7affda - Change sortOnDisk option to sortInMemory 
- Fix horrible cleaner bug
- Trivial optimizations to cleaner code - more significant ones coming soon.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2850 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-17 20:52:57 +00:00
ebanks 476d6f3076 RealignerTargetCreator is officially live 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2697 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 03:41:52 +00:00
aaron a34c2442c0 moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2460 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 07:40:48 +00:00
hanna 2bd0b1bbf7 After further review, it's unclear that my patch in RecalDataManager was the right choice. Reverting. 
Also updating other IntervalCleanerIntegrationTest failures that were masked by my first patch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2440 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-24 00:32:33 +00:00
hanna 98c268483e Fixed issues with the integration tests: 
1) sam-jdk apparently no longer supports custom tags with type int[] values.
2) BAM output for indel cleaner integration test changed in a way that's so subtle it can't be seen after converting the output to .sam.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2439 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 23:12:22 +00:00
ebanks 87e5a41964 Fixed a bug that accounted for a bunch of my remaining mis-cleaned indels. 
Also, slightly optimized the cleaner by using readBases (instead of readString) and caching cigar element lengths.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2419 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-21 05:46:16 +00:00
asivache e6cc7dab26 fixing md5 sum; new version of IndelIntervalWalker does the right thing... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2388 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-17 01:04:13 +00:00
hanna 7c386fa428 Another case of reordering of read groups blowing up checksums. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2030 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 00:07:35 +00:00
aaron 2e4949c4d6 Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1751 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-30 20:37:59 +00:00
ebanks 1362a56227 Added fasta tests and small fix to cleaner test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1575 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-10 03:13:11 +00:00
ebanks bed646e4f6 Adding cleaner test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1561 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 16:05:56 +00:00
aaron 0df6a9da5c -Seperating out normal (unit) tests and integration tests. From now on if your test are more of an integration test (i.e. you're testing a walker and all the subunits it relies on) please name the test "______IntegrationTest.java" instead of "______Test.java". 
-Bamboo will now run the integration tests once a day, and the normal units tests on each check-in.

-Also added a bunch of unit tests for VariantEval walker

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1555 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 15:01:40 +00:00
ebanks 0cc219c0df -Added unit test for walkers dealing with intervals for cleaning 
-I also uncovered a corner case in the cleaner that for some reason was commented out but shouldn't have been.  Hooray for unit tests!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1553 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 02:35:17 +00:00
hanna ccdb4a0313 General-purpose management of output streams. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1454 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-23 00:56:02 +00:00
hanna 7a13647c35 Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very* 
rough initial implementation, but should provide enough support so that people can stop
creating SAMFileWriters in reduceInit.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1332 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-29 16:11:45 +00:00
hanna 2db86b7829 Move the cleaned read injector test from playground to core. Remove CovariateCounterTest's dependency on the CleanedReadInjector. Start doing a bit of cleanup on the CLP's FieldParsers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1312 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-24 19:44:04 +00:00