1f820d5026
Added two files from some refactoring changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5205 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-06 19:20:12 +00:00
1085bbf303
Fixed issue where all comp tracks were being treated as known tracks. Fixed issue where multiple JEXL expressions were causing an exception because the underlying object did not implement the Comparable interface. Fixed issue where variants being compared to the known track were not being checked for equality of variation type. Fixed issue where functional annotations were not being iterated over properly. Refactored a lot of helper methods into a separate VariantEvalUtils utility class. Significantly expanded the test suite using a small VCF with SNPs, indels, and non-variant loci which makes it much easier to see what the proper answer should be, and included the appropriate grep and awk commands in the comments to confirm the values.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5204 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-06 19:19:20 +00:00
c4707631e2
MethodsDevelopmentPipeline is now the test bed for large scale AWS_S3 logging. Can be disabled from command line if this is necessary
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5203 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-06 17:03:45 +00:00
8b8b4fced1
Removed explicit memoryLimit, so that memLimit given on the command-line will NOT be ignored...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5202 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-06 01:55:17 +00:00
cc5d695bcf
Renamed the IPFL Test to IPFL PipelineTest so that it'll be picked up by the PipelineTests.
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HACK: Turned off JNA autoRead() in the jobInfoEnt LSF structure to try and dodge the SIGSEGV during strlen calls during bmods.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5201 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-05 00:06:12 +00:00
ce51ffb56e
Oops, old local paths committed on accident.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5200 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 23:35:56 +00:00
29f3ad72f3
SAMFileWriter that allows the user to move reads, but only a bit, in an incoming coordinated sorted BAM files. Does some local reordering and local mate fixing, under specified constrained. These constrains allow us to make a special -- under testing for Eric, who promised to try this out a bit, expand test cases and integration tests -- but soon to be the default and only model of the realigner that only moves reads with ISIZE < 3000 that directly emits a coordinate sorted, mate fixed validating BAM file without needing FixMates externally. Preliminary testing shows this runs in a totally fine amount of memory and produces equivalent results to the previous version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5199 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 22:27:05 +00:00
11ea321b39
Trivial header cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5198 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 22:23:15 +00:00
fe4aa58d35
Removing unused class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5197 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 22:22:28 +00:00
0ad1ea4aa1
Fixed Umapped misspelling
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5196 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 22:21:41 +00:00
03f265d8bd
Change DP format field description in the header line (expected count=1)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5195 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 21:28:25 +00:00
4cdc974c5f
Preliminary Qscript to run DoC for the purpose of CNV detection
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5194 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 21:25:59 +00:00
c0e998621c
Computes two format (genotype) level annotations: total read depth in the given sample (DP format field) and fraction of reads supporting alt allele(s) in the given sample (FA format field)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5193 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 21:23:55 +00:00
8700b74640
Now annotates indels as well. Probably can also annotate mixed vcf with indels +snps, but not tested in that mode...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5192 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 20:28:03 +00:00
cd6ace1b47
Includes UG version of indel genotyping rather than IGV2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5191 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 20:25:46 +00:00
bfc6ef1753
A successful attempt at a queue integration test, ensuring that the InProcessFunction libraries are working as expected.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5190 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 21:30:35 +00:00
358a400474
made ApplyVariantCut a default part of the pipeline, added the -noCut option if you don't want to use it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5189 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 19:29:36 +00:00
ce2866122d
Calls the bams pulled down from firehose cleaned by default
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5188 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 18:34:07 +00:00
a22ea53665
Updated template for the MPG pipeline's queue script runner.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5187 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 18:33:29 +00:00
9fc45e1234
Use the yaml as an arguemtn to get out squid numbers
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5186 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 18:32:05 +00:00
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
kiran
depristo
fromer
kshakir
asivache
corin
chartl
carneiro
hanna
ebanks
rpoplin