zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
9,274 Commits
1 Branch
0 Tags
257 MiB
Commit Graph

56 Commits (f9f8589692fece0185a7e8e059b75ee4672d1c8d)

Author SHA1 Message Date
Mark DePristo b0560f9440 Rev. tribble to fix BED codec bug in tribble 51 2012-01-17 16:40:26 -05:00
Mark DePristo f2b0575dee Detect unreasonably large allele strings (>2^16) and throw an error 
-- samtools can emit alleles where the ref is 42M Ns and this caused the GATK (via tribble) to hang in several places.
-- Tribble was updated so we actually could read the line properly (rev. to 51 here).
-- Still the parsing algorithms in the GATK aren't happy with such a long allele.  Instead of optimizing the code around an improper use case I put in a limit of 2^16 bp for any allele, and throw a meaningful exception when encountered.
 2012-01-17 16:40:26 -05:00
Matt Hanna c9eae32f6e Revving Tribble to actually close file handles when close() is called. 2011-11-30 22:42:21 -05:00
Eric Banks d7d8b8e380 Tribble v42 changes the Codec.canDecode method to take in a String instead of a File; this is something that Jim was adamant about (because Tribble can handle streams other than files). I didn't want the next person who needed to rev Tribble to deal with this change additionally, so I took care of updating the GATK now. 2011-11-28 14:18:28 -05:00
Eric Banks d64f8a89a9 Instead of the SelfScopingFeatureCodec interface, pushed this functionality into Tribble itself. Now we can e.g. determine that a file can be parsed by the BedCodec on the fly. 2011-11-09 15:24:29 -05:00
Eric Banks 6297561326 Adding the new jar 2011-11-07 15:08:19 -05:00
Eric Banks aa0c8c3600 Revving Tribble jar to v40. Our last jar was busted. 2011-11-07 11:30:08 -05:00
Mark DePristo 34f435565c Accidentally committed unclean tribble jar to repo 2011-09-21 10:16:17 -04:00
Mark DePristo 827c942c80 Rev tribble 2011-09-20 14:01:14 -04:00
Eric Banks da9c8ab386 Revving the Tribble jar where the DbsnpCodec class was renamed to OldDbsnpCodec. Updating GATK code accordingly. 2011-09-06 20:39:42 -04:00
Mark DePristo 0b794b5491 Reving Tribble to 23 2011-09-01 10:43:03 -04:00
Mark DePristo d604019362 Finished my broken tribble code. Updated to rev 22 2011-08-30 16:56:48 -04:00
Mark DePristo 173ca1e215 Reverting tribble temporarily while I fix my subtle problems 2011-08-30 11:08:13 -04:00
Mark DePristo 427c643ce7 The missing tribble jar 2011-08-29 18:46:40 -04:00
Mark DePristo 5defaf5fac Continuing to improve Tribble 
-- ProfileRodSystem now has a just load index mode, allowing us to optimize the profiler
-- assessFarmNodes R script for making nice plots of performance of jobs on the farm
-- Rev. tribble to use new, optimized index loading (performance win when loading many many indices)
 2011-08-29 17:02:57 -04:00
David Roazen bd5cdb8a43 The tribble dependency is now handled through ivy. Revved tribble to r18 and removed obsolete build targets in build.xml 2011-08-11 16:38:29 -04:00
Mark DePristo 35ec82a467 Oops, need this 2011-07-17 13:08:08 -04:00
Mark DePristo 4db2b13e9e Rev tribble. 
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
Mark DePristo a5bfcb1ed9 V15 is broken. Going up to v16 in a second. 2011-07-17 10:25:34 -04:00
Mark DePristo 2b55d5b7c0 Test tribble library where equals() ignores time stamps. 2011-07-16 16:45:55 -04:00
David Roazen 07b875c779 Renaming the updated tribble jar file to match the svn revision number. 2011-07-16 09:57:46 -04:00
Mark DePristo 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
David Roazen 643458d7db Updated the tribble jar -- this should fix most of the integration test 
failures we've been seeing.

Note that with tribble's new svn repository the revision numbers have reset,
hence "revision 3"
 2011-06-29 01:11:03 -04:00
droazen 171e20a111 Updated the tribble jar to revision 351 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6068 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-22 22:55:57 +00:00
droazen ab1de3bfda Updated the tribble jar to revision 350 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6065 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-22 22:55:46 +00:00
droazen 95614ce3d6 Updated the tribble jar to revision 345 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6033 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-22 22:53:25 +00:00
droazen 32a991c4d3 Updated the tribble jar to revision 343 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6031 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-22 22:53:17 +00:00
droazen 480598842c Updated the tribble jar 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5982 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-13 18:00:09 +00:00
aaron b3fd145161 fix for a bug deep in the tribble indexing: if you had a single record in the first contig, the second contig's index blocks would point to the wrong file seek location, and you'd see no 
features in that contig. Thanks to Mark for finding this.  I'm not rev'ing the index version (which would cause all indexes to be rebuilt), since this seems like a pretty rare edge case.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3865 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-23 18:39:55 +00:00
aaron 9579aace1f updates to code dependent on Tribble, as well as the following Tribble changes: 
- makes writing to disk optional for indexes using the indexCreator classes (allow the user to specify the index file, if null don't write it)
- removed some system.out debugging code
- fixed version checking in interval tree 
- made indexes store and return a LinkedHashSet for sequence names (to ensure they've preserved the ordering in the file)
- index creators now read the file before creating the index
- changed the Index.write() method to take a LEDataStream instead of a file
- removed the sequence dictionary code on the header
- added utils for getting LEDataStreams
- added a base Tribble exception




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3857 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-23 01:56:10 +00:00
aaron 1cba81c16f updates to tribble with fixes for some bugs I've found in some new indexing code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3842 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-20 22:08:04 +00:00
aaron af6b5f000e updating the Tribble library; added writing of indexes to the index interface for working with the tree index. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3836 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-20 07:02:08 +00:00
aaron 250ab70fed update the Tribble library too. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3827 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-19 05:00:37 +00:00
aaron dff4c06763 Rev'ing Tribble with a special version that has excluded VCF 3.3 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3640 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 18:20:51 +00:00
aaron 54ae0b8e4e some updates to tribble for the svn commit that will follow 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3621 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-23 20:20:07 +00:00
aaron 5b87a00a5f updating with associated Tribble changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3605 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 07:54:15 +00:00
depristo 57a13805da GATK now uses a optimized indexing scheme in Tribble. 5x or more performance gain on files with many genotypes. Updated integrationtest that was failing and was clearly wrong. DB=; isn't a valid annotation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3596 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-19 21:36:41 +00:00
aaron 32f6781ac7 updating tribble with the VCF header changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3583 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-18 08:20:44 +00:00
ebanks 8c28be5933 Fixing a VCF bug for Sendu: we weren't emitting flags (booleans) correctly in VCF3.3 (rev'ed tribble for this). 
Updated dbsnp/hapmap membership info fields to be flags now instead of ints.
While I was there, I added the change in the Annotator for Jan to force reads to be from a specific sample.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3536 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-11 16:42:06 +00:00
aaron e27951ab39 re-updating the VCF code to handle spaces in sample names 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3528 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-10 20:18:34 +00:00
aaron ad98512f6c adding changes so that we look at the headers already loaded by the engine for samples and other VCF utils, and not create readers for each file to get them (this caused Tribble to regerenate indices if the index file can't be written to disk). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3518 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 17:21:12 +00:00
aaron 6febd0291d rev tribble to include some dbsnp clean-up and fixes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3510 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 03:08:31 +00:00
aaron 6d5556939d updating Tribble with a couple of important Tabix fixes, and updating the variant eval integration tests to run each test with both plain vcf and gzipped tabix (added the tabix version 
to the vlidation directory), using the same md5sum.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3509 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 01:47:04 +00:00
aaron 0b03e28b60 updating the tribble library to include the reference dictionary reading / writing. We now check the dictionaries of any tracks that have them against the reference (all new tribble tracks and out-of-date tracks will have this). Also renamed some classes to be more reflective of their function. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3485 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-04 06:34:26 +00:00
ebanks ffeb3fd80d Thanks to Guillermo, I found a bug in the Unified Genotyper output: GL was posteriors instead of likelihoods. Not a huge deal because the 
priors were flat, but fixed nonetheless.
Also, needed to update Tribble.
Minor updates to the Beagle input maker.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3461 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-28 19:28:26 +00:00
aaron 98350da177 rev tribble 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3456 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-28 14:52:39 +00:00
aaron f7c9f131ea revisioning tribble to version 85, which includes tabix and bug fixes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3428 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-25 04:28:32 +00:00
aaron 7cfb9ff3dc updates for Tribble 82, fixes for Ryans case where multiple processes would attempt to read/write to the same index, and a couple other Tribble-centric bug fixes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3382 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 19:34:45 +00:00
aaron 2c55ac1374 fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3349 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-12 06:13:26 +00:00
aaron 7d2df3f511 example windowed ROD walker for Kristian, and updates to Tribble 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3325 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 17:12:50 +00:00