depristo
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7ad8fbdd5a
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Moved GATKException to exceptions
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4266 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-12 14:47:19 +00:00 |
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depristo
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595907e98e
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Moving StingException
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4262 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-12 14:34:15 +00:00 |
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depristo
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40e6179911
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Penultimate step in exception system overhaul. UserError is now UserException. This class should be used for all communication with the USER for problems with their inputs. Engine now validates sequence dictionaries for compatibility, detecting not only lack of overlap but now inconsistent headers (b36 ref with v37 BAM, for example) as well as ref / bam order inconsistency. New -U option to allow users to tolerate dangerous seq dict issues. WalkerTest system now supports testing for exceptions (see email and wiki for docs). Tests for vcf and bam vs. ref incompatibility. Waiting on Tribble seq dict improvements to detect b36 VCF with b37 ref (currently cannot tell this is wrong.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4258 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-12 14:02:43 +00:00 |
rpoplin
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e3962c0d13
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VR integration tests are longer but much more useful.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4210 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-03 15:50:19 +00:00 |
ebanks
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71c4d3f33d
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Moving pointer to b36 reference from /broad/1KG to /humgen/1kg
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4021 348d0f76-0448-11de-a6fe-93d51630548a
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2010-08-13 00:54:34 +00:00 |
aaron
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d514c424fd
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adding tests for BTI in the ROD validation tests
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3997 348d0f76-0448-11de-a6fe-93d51630548a
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2010-08-10 06:05:40 +00:00 |
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ebanks
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340bd0e2c1
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Removed hard-coded pointers to references
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3934 348d0f76-0448-11de-a6fe-93d51630548a
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2010-08-04 17:59:37 +00:00 |
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aaron
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32f324a009
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incremental changes to the VCF4 codec, including allele clipping down to the minimum reference allele; adding unit testing for certain aspects of the parsing. Not ready for prime-time yet.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3604 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-22 06:31:05 +00:00 |
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aaron
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8ec091d6d2
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re-enabling regeneration of the tribble index if it's out of date. Also moved the class that can detect text in the log4j stream (useful in testing to make sure appropriate messages are generated).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3480 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-02 17:45:51 +00:00 |
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depristo
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64ccaa4c6a
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Walkers and integration tests that calculate and compare callable bases
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3328 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-07 21:33:47 +00:00 |
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ebanks
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71f38a9199
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Adding performance tests for the recalibrator (Whole Genome and Whole Exome tests).
Should take ~3 hours to run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3145 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-09 18:30:59 +00:00 |
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depristo
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197dd540b5
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added root GATKData variable
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2831 348d0f76-0448-11de-a6fe-93d51630548a
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2010-02-12 15:25:34 +00:00 |
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aaron
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a34c2442c0
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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
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2009-12-29 07:40:48 +00:00 |
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aaron
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b840dd1320
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Added some code to change the instrumentation for tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@756 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-20 05:15:27 +00:00 |
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depristo
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8e9e2f4502
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Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@716 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 21:06:28 +00:00 |
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aaron
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98f4920739
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Added BCEL and some basic instrumenation code to the test library.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@602 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-06 17:18:23 +00:00 |
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aaron
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96248cdec4
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Added some output to all the classes, including build in runtime analysis
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@411 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 19:14:53 +00:00 |
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aaron
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88ebf1a05b
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Fied some documentation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@406 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 17:41:38 +00:00 |
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aaron
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704f1bd634
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It helps if I check the new base class in with my changes
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@404 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 17:18:16 +00:00 |