80b5c5261a
CombineVariants no longer combines records of different types. So now when combining SNP and indel callsets, overlapping calls get their own records. Useful for Khalid in the pipeline. For those interested, it turns out the previous behavior was doing the wrong thing occasionally (and this was even captured in the integration tests).
2011-07-18 13:42:45 -04:00
bc8b5da698
Added docs while I was reading through the code to understand it
2011-07-18 12:25:54 -04:00
d8517a000a
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-18 11:07:18 -04:00
f15357c2e1
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-18 10:52:31 -04:00
95c776bf59
Updated documentation.
2011-07-18 10:52:06 -04:00
cb9bef6847
Updated documentation.
2011-07-18 10:51:22 -04:00
51b0dd01c3
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-18 10:47:29 -04:00
449bf1b539
Testdata for diffObjects.
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PipelineTest updated to point to MD5DB.java
2011-07-18 10:47:03 -04:00
d6e2e89f99
Walker test system refactoring. All MD5DB related functions are now in MD5DB.java.
...
System has the concept of a local and a global MD5 db. The local one is like it operated previously. The global one lives in /humgen/gsa-hpprojects/GATK/data/integrationtests. If the system can find this directory then MD5s will also be read / written to this location. This means that gsabamboo will print differences as appropriate. And all users will in effect have access to a complete history of MD5 file results.
A few minor code reshuffles changed VariantRecalibration and VCFHeader test files.
2011-07-18 10:46:01 -04:00
6f26c07b85
Removed the SpecificDifference class. Now Difference classes always have the option to remember specific master and test values. This means that all summarized differences carry with them specific examples of their differences. Consequently, now even summarized differences give at least one example of the specific difference, even when the count of the difference is > 1. Unit tests updated. Added DiffObjects integrationtest. VCFDiffableReader now specifically reads the first line of the VCF file to capture the version number.
2011-07-18 10:42:35 -04:00
1f538d2add
Place the preQC database in /humgen/gsa-scr1/GATK_Data.
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Rework the way data outside the center 95% is trimmed out.
Cleanup some documentation.
2011-07-18 10:33:57 -04:00
837a91b85d
No more ls to stdout unless verbose is true [manageGATKS3Logs.py]
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Fully qualified paths now work properly. Moved script into git [downloadGATKReportsFromS3.csh]
Correct path to files in runGATKReport.csh
2011-07-18 08:31:08 -04:00
094f032a1e
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-18 08:08:48 -04:00
b2b7d27fed
Merge branch 'laptop'
2011-07-18 00:25:46 -04:00
497721a799
Added class documentation string.
2011-07-18 00:25:21 -04:00
ac9c66138d
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-18 00:20:33 -04:00
c9878b9286
Supports the new GATK release naming scheme: 1.0-6145-g1af7673. Now looks at 1.0- (or appropriate) and scores all of these directories as part of the same release.
2011-07-17 22:58:18 -04:00
824100e57f
Corrected typo in MergeAndMatchHaplotypes integration test
2011-07-17 22:50:54 -04:00
8167aba601
Moved (poorly named) MergeAndMatchHaplotypes to public. Added integration test
2011-07-17 22:47:32 -04:00
afb506e128
Added MD5s for PhaseByTransmission integration tests
2011-07-17 21:55:33 -04:00
558e197989
Integration test for PhaseByTransmission
2011-07-17 21:25:08 -04:00
cda90f66fe
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-17 20:59:12 -04:00
00b650a35d
Get rid of accidental commit of emacs backup '~' file.
2011-07-17 20:52:46 -04:00
567ed66085
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-17 20:44:43 -04:00
0a0363aef2
Revving Picard to get a parser that works with the latest metrics file formats
...
we're starting to see.
2011-07-17 20:43:35 -04:00
66575b7644
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-17 20:31:25 -04:00
9992c373be
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
2011-07-17 20:29:58 -04:00
4ea433f8e1
Moved PhaseByTransmission to public
2011-07-17 19:42:00 -04:00
5da278d926
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-17 19:33:19 -04:00
f36641721c
Basic functionality for reading a VCF file into R.
2011-07-17 19:31:33 -04:00
eac127e66a
Reverted PhaseByTransmission to an earlier form that does not try to incorporate RBP information while phasing genotypes by transmission. Also restored a line that ensures the samples get emitted to the VCF file in sorted form.
2011-07-17 19:15:52 -04:00
ecc8726f63
Merged bug fix from Stable into Unstable
2011-07-17 18:10:18 -04:00
9ca9cf52ac
Uncommenting a stray commented test.
2011-07-17 15:38:33 -04:00
35ec82a467
Oops, need this
2011-07-17 13:08:08 -04:00
4db2b13e9e
Rev tribble.
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Just added more documentation for diffEngine and pointer to new wiki:
http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
2011-07-17 13:05:04 -04:00
1af76736b9
Guarantees that the list of files will always be in the same order.
2011-07-17 11:41:34 -04:00
a5bfcb1ed9
V15 is broken. Going up to v16 in a second.
2011-07-17 10:25:34 -04:00
92a1c0c278
Moved the varianteval/tags/DataPoint.java and varianteval/tags/Analysis.java to varianteval/utils. This allows rsync to see these files with the -C option, as tags is some kind of reserved CVS keyword.
2011-07-17 10:14:23 -04:00
2b55d5b7c0
Test tribble library where equals() ignores time stamps.
2011-07-16 16:45:55 -04:00
07b875c779
Renaming the updated tribble jar file to match the svn revision number.
2011-07-16 09:57:46 -04:00
9fe68776c0
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-16 09:22:55 -04:00
eacf205f40
Tests needed to be updated to reflect the code reorg of tribble.
2011-07-16 09:22:34 -04:00
7524b00cbc
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-16 09:12:13 -04:00
6e8ec206c8
Now with clean output. Ready to go live in crontab.
2011-07-16 09:11:49 -04:00
e106a5e734
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-16 08:52:18 -04:00
5e7bc862a3
Rev tribble to include new equal() method that prints out details of why two indices are not the same.
2011-07-16 08:51:21 -04:00
5cb5a4ec75
Merged bug fix from Stable into Unstable
2011-07-16 00:23:59 -04:00
dd92a14b40
Made extra indel VCF optional but DBSNP mandatory.
2011-07-16 00:23:35 -04:00
2fa5dbb0fe
Merged bug fix from Stable into Unstable
2011-07-16 00:15:19 -04:00
ed55182a4c
Removing Broad specific paths from parameters and making them required. This should make it unambiguous for people inside and outside the Broad to use the DataProcessingPipeline (as per request in the GetSatisfaction)
2011-07-16 00:09:00 -04:00
Eric Banks
Matt Hanna
Mark DePristo
Kiran V Garimella
Mauricio Carneiro
David Roazen