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
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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
9579aace1f
updates to code dependent on Tribble, as well as the following Tribble changes:
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- 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
1cba81c16f
updates to tribble with fixes for some bugs I've found in some new indexing code.
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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
af6b5f000e
updating the Tribble library; added writing of indexes to the index interface for working with the tree index.
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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
250ab70fed
update the Tribble library too.
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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
dff4c06763
Rev'ing Tribble with a special version that has excluded VCF 3.3
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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
54ae0b8e4e
some updates to tribble for the svn commit that will follow
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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
5b87a00a5f
updating with associated Tribble changes
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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
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.
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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
32f6781ac7
updating tribble with the VCF header changes
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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
8c28be5933
Fixing a VCF bug for Sendu: we weren't emitting flags (booleans) correctly in VCF3.3 (rev'ed tribble for this).
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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
e27951ab39
re-updating the VCF code to handle spaces in sample names
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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
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).
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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
6febd0291d
rev tribble to include some dbsnp clean-up and fixes
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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
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
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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
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.
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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
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
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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
98350da177
rev tribble
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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
f7c9f131ea
revisioning tribble to version 85, which includes tabix and bug fixes
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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
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.
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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
2c55ac1374
fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation.
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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
7d2df3f511
example windowed ROD walker for Kristian, and updates to Tribble
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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
78409dca0d
turned off the progress output from tribble when making an index, and fixing a case where the index file isn't writable so we instead make the index in memory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3312 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 16:36:58 +00:00
d91b27aca1
updating Tribble with VCF changes from Eric
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3310 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 04:03:21 +00:00
97dd04cbf0
updating Tribble ahead of the big VCF commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3297 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 05:17:54 +00:00
447081583a
rev tribble with updated version
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3287 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 04:07:28 +00:00
b648e89096
updating Tribble with a bunch of bug and performance fixes found while performance testing GeliText in the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3267 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 18:45:10 +00:00
8fd3351971
adding a stripped down Tribble library for the start of integration
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2851 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-17 21:29:25 +00:00
aaron
depristo
ebanks