b1ff371c8f
Peek inside the StingText.properties to make sure the version in the properties matches the build version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5185 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 18:07:55 +00:00
5c3198520c
A few minor modifications masquerading as significant changes according to
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svn's logs:
- Copied BAM indexing engine from Picard back into the GATK anticipating
shard merging algorithm. Tried to leave most of the building blocks in
Picard. If this turns into a logistical nightmare, I'll merge the building
blocks into the GATK as well.
- Reorganized the org.broadinstitute.sting.gatk.datasources package, giving
better separation of query and management functionality for reads, ref, rmd,
and samples.
- Merged Shard building blocks into org.broadinstitute.sting.gatk.datasources.
reads package, indicating it's current strong relationship with the reads,
rather than the general unifying element I wish this would be.
- Collapsed BAMFormatAwareShard into Shard.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5184 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 17:59:19 +00:00
7af003666d
added optional argument -cut to apply the variant cut to the ts recalibrated vcf.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5183 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 17:34:40 +00:00
5398cf620a
Bug fixes in the in process function (spoiled by python: was not closing my writers). SortByRef now works somewhat like the perl script does, rather than doing a memory-expensive sort. Adding a QTools qscript which is kinda clunky, and will be used mostly for integration tests of these IPFs, pending some better way to construct argument collections and function accessors at compile-time.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5182 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 17:32:46 +00:00
9ddc95c833
NewEvaluationContext needs to be generated in the inner loop. Otherwise, multiple comp tracks end up getting routed to the same row of the output table. Added test to cover multiple comp tracks.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5181 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 07:04:53 +00:00
a9d0921529
That variable name could only lead to trouble.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5180 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 05:03:48 +00:00
9515f94242
Commiting a simple merge IPF for use with qscripts (currently use a long grep, awk, pipe command, which can be unsafe and is hard to extend). Tests for all these functions coming soon. Also, IntelliJ + intermittent VPN connection = botched repository.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5179 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 05:01:21 +00:00
918cc09477
Allow multiple records at a position
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5178 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 04:19:05 +00:00
cb6454bf98
Multiple eval tracks should be bound with different names, rather than just 'eval'. Added tests to cover usage with multiple tracks.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5177 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 22:33:50 +00:00
cf15819db5
updated to work with the new VariantEval.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5176 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 17:46:07 +00:00
47357b726e
Fixing import GenotypeCalculationModel since it doesn't exist anymore.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5175 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 15:39:43 +00:00
5a8e2c2739
Going through the backlog of emergency hacks I put in for the 1000G release. It is possible to call a site in an analysis panel but when using all samples the site isn't called because of going over the minimum deletion threshold, for example.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5174 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 15:12:26 +00:00
7605f0e6c1
Corrected input/output definitions for Queue
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5173 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 07:39:00 +00:00
3839fd1a25
Updated phasing pipeline to properly read samples from VCF and BAM files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5172 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 07:16:05 +00:00
43fb11b923
Removing stray non-ASCII character
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5171 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 03:10:08 +00:00
2732c839d4
Restored parallelism and associated tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5170 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 02:04:03 +00:00
fd8dd8fb9b
Fixed an issue where a no-call in the eval track would prevent a site from a comparison track from being loaded. Added a new test to cover the use case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5169 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 01:47:53 +00:00
aab0ec209b
small bug fix on chromosome names.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5168 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 20:55:19 +00:00
798955b006
After discussing with Mark, revert to "Master merging" of phase information from VCFs. This has the advantage of creating minimal phased VCFs from RBP, from which phase info is merged into the original "master VCF". Also, updated Genotype.sameGenotype() to be simpler and NOT REVERSE the ignorePhase flag in comparing Allele lists/sets
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5167 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 19:50:15 +00:00
dac83d21bc
Fixes for IndelLengthHistogram for someone on GS. This evaluator apparently doesn't have an integration test. I'll fix that tonight.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5166 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 19:48:09 +00:00
06b63d8336
Pulled out CpG stratification in test results at Kiran's suggestion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5165 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 18:36:09 +00:00
25f045cac6
Changing locking errors to warnings. This will hopefully allow us to diagnose
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the mysterious failure in STING_INTEGRATION-3832, the next time it appears.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5164 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 16:29:31 +00:00
027c91871f
Commenting out something I meant to leave commented out
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5163 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 15:47:52 +00:00
91297c138b
Update VCFStreamingIntegrationTest to use new variant eval command-line
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arguments, output format.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5162 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 15:40:43 +00:00
7d89ce820b
Got tired of waiting for Kiran to fix the build: updated NewVariantEval ->
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VariantEval.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5161 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 15:32:39 +00:00
96241c6637
More testng fallout: fixing another seemingly 'random' issue arising from an
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alternate test ordering.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5160 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 15:25:50 +00:00
e510798bc2
Missed one uncomment
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5159 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 13:01:59 +00:00
d9532ecf53
Better run reporting structure. Now text report is attached as well as inline in the email, so you can easily view it in fix width fonts!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5158 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 12:58:48 +00:00
393df46055
updates to handle only reporting on a specific SVN revision. Updated the R script to show the domain name of the runner, now that S3 logging is working
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5157 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 12:02:12 +00:00
e5e65ecfbe
Bugfix for GetSatisfaction: ensure that the two statistics objects (the map, and the pair) are actually pointers to the very same object.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5156 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 06:40:42 +00:00
34f5587f2c
As with the cleaner, don't exception out when trying to get the GATK version after -Ddisable.help=true
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5155 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 06:08:59 +00:00
4243f0dea7
1) Fix for Tim et al: HashMaps don't necessarily return objects in a deterministic fashion when keys are pointers; break it apart into a list.
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2) Fix for Kiran: when running with -Ddisable.help=true, don't exception out when trying to get the GATK version.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5154 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 06:06:48 +00:00
5279ef24a3
Fixed typo that kept scala tests from recompiling.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5153 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 02:41:07 +00:00
a89400b20c
Simple implementation to retrieve relevant BAM files for each sample
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5152 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 00:03:03 +00:00
e74f28ad89
If there's an LSF queue maximum time limit set and the user hasn't specified one for this job, pass on the queue defined maximum limit with the job.
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Updated LibBatIntegrationTest to use proper networked temp directory accessible by local machines and nodes.
Disabling the FCPTest until the VE3 is incorporated into the fullCallingPipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5151 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 23:13:09 +00:00
f258363cfc
Minor bug fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5150 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 22:29:28 +00:00
742bd44728
Changed output file to be user-defined
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5149 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 22:15:26 +00:00
391f248640
Inserted a dangerous (but hidden) command-line argument for use by the Picard team.
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Used to process intervals over BAMs without indices. Tim understands the risks but
wants this anyway, as a temporary solution to a pipeline problem.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5148 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 22:10:06 +00:00
6c99dc4dab
Take (partial) ownership of phasing 1000G chr20 calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5147 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 21:49:41 +00:00
1753f9d864
"Properly handles multiplexed and non multiplex lane data from the picard database."
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5146 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 21:14:32 +00:00
4cb910bc38
Fixed import statements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5145 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 19:26:37 +00:00
4d9bc84bd5
Initial commit of in-process helper functions for making the BCM more robust
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5144 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 19:18:31 +00:00
d4f744a4d4
Checking if the interval files exist before using them to calculate the minimum scatter parts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5143 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 18:07:34 +00:00
b7aac3b846
Corrected import statement to reflect VE3's new position in core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5142 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 18:01:02 +00:00
3f387bc8d8
Transitioned over to VE3 architecture.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5141 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 17:54:18 +00:00
401feca90d
Updates to VariantEval 3.0 integration test.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5140 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 17:45:06 +00:00
cab426f86f
VariantEval 3.0 is now in core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5139 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 17:42:08 +00:00
c59b2a8296
Removed experimental "master merging" from CombineVariants
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5138 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 17:13:05 +00:00
b0432ee1e2
First part of a two-stage commit. Removing old VariantEval to make room for VariantEval 3.0 in core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5137 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 17:03:41 +00:00
d406d9b3fc
There's no reason to special case no-calls if they already have PLs associated with them. Just use the PLs!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5136 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 15:05:45 +00:00
kshakir
hanna
carneiro
chartl
kiran
ebanks
rpoplin
fromer
corin
depristo