136c8c7900
ClipReads now supports HARDCLIP_BASES, though in fact this turned out to be not necessary for my desired tests. In the process of developing the HARDCLIP mode, I added some proper ReadUtils unit tests, which would ideally be expanded to include other ReadUtil functions, as added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5890 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 11:42:22 +00:00
549172af10
removing dependance on jobQueue == gsa
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5889 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 10:12:09 +00:00
a77ca2d36a
Incorporating Guillermo's patch to eliminate compile-time dependency of (core) UG indel model
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on oneoffs. Thanks Guillermo! We'll polish the patch when you free up a bit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5888 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 02:22:19 +00:00
fd21c5d100
Minor update so the debug messages don't show temp files as chromosome 208799060637697164972
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5887 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 22:56:33 +00:00
b4af28c7df
Handle case where -L argument (intervals) not given
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5886 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 20:24:56 +00:00
a561d3adc7
Utitlity function to for plotting post-run qc metrics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5885 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 20:14:25 +00:00
fccd5517a0
Generates post run QC plots with by sample metrics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5884 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 20:13:59 +00:00
59495c7f03
Updated tearsheet function utility
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5883 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 19:58:57 +00:00
8a57c52005
Produces a more throurough tearsheet with detailed metrics and information
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5882 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 19:57:49 +00:00
1e2892a35d
Preliminary QC script in R, which checks coverage, fingerprints, library duplication, total SNPs, dbSNP%, and availability of sample data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5881 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 19:57:00 +00:00
6ecbfa9013
OK, this time REALLY fix cut and paste error
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5880 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 19:47:12 +00:00
dab269160b
Added cofoja to the Queue package. Although BCEL doesn't think they're needed the scala compiler respectfully disagrees.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5879 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 17:42:34 +00:00
efe6602827
Fix copy-paste error from previous commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5878 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 16:02:08 +00:00
7a43673599
Bug fix: also enclose fetching FS or HRun in a try/catch block or else code will blow up if an annotation is absent (e.g. when there no evidence for a variant in a vc)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5877 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 15:00:36 +00:00
f7298f4a7f
First of many baby steps to redo way in which we trigger events for indel calling and to eliminate extended events: get rid of SpanningDeletions annotation for indels. It's completely useless, and even more so once we no longer trigger at extended events (because we'll trigger by definition a base before a deletion starts, so deletions present in the current pileup are not informative).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5876 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 00:49:23 +00:00
d393f59ad2
Moving the hg19 reference to a new location as per instruction from our intrepid leader
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5875 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-25 17:48:59 +00:00
bafdd4f8f7
Ask for existance of extended pileup before grabbing it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5874 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-25 17:39:03 +00:00
9d8c963fcc
Switched arguments from short name to long name.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5873 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-25 17:24:56 +00:00
6ec3dd0f8c
Updated GridEngineJobRunner to return status RUNNING instead of PENDING when a job has been sent to GridEngine, even if it hasn't started.
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Added GridEngine to pipeline tests.
Removed passing -jobProject since GridEngine projects must be predefined.
Writing the HybridSelectionPipelineTest yaml into the temp directory.
Disabled job priority as it needs to be refactored for use by GridEngine and LSF.
Fixed WholeGenomePipeline variantmergeoption rename to filteredRecordsMergeType.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5872 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-25 17:16:44 +00:00
3565eca2dd
Script to run UG to create annotated all-pop VCF files to use for Phase1 VQSR indel project consensus. Paralleles and generalizes SNP version, so in theory this script can be used for both SNP and Indel consensus.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5871 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-25 16:50:59 +00:00
3d134a8497
Updated to produce (actual) hg19 resources too
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5870 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-25 02:14:55 +00:00
389c546757
Renamed for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5869 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-25 02:12:21 +00:00
6ed71cf683
Annotation that adds a list of samples who are polymorphic at a site based on the GTs. Very useful if you are looking at rare variants among many samples, esp. in Evoker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5868 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 20:12:27 +00:00
1bd1404aa9
Sometimes md5s can be null
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5867 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 19:17:18 +00:00
e6396062c0
Script to use VQSR on indels - does VR, AR on each continental group, combines variants and then does VariantEval comparing with different chr20 all-pop 1000G callsets.
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Not for general use yet!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5866 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 17:19:30 +00:00
e582a92af6
WalkerTest now checks for valid md5s in the integrationtests themselves, so no more stray whitespace errors. Added a WalkerTestTest to ensure tha t bad MD5s are detected and an error thrown
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5865 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 14:34:55 +00:00
0448ef28d3
Actually use the right parameter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5864 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 12:09:01 +00:00
06486c134a
Kill extra space in the md5.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5863 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 12:00:31 +00:00
d551ce720d
Updated with new CombineVariants syntax
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5862 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 11:38:09 +00:00
57e4693e4c
Slightly better error message when failing to create the index on the fly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5861 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 11:04:08 +00:00
cf3dbfee97
Renamed variantMergeOptions to filteredRecordsMergeType, as this is really what it does. Cleaned up the wiki so that it's clear what this does, as well as included an example of how to create an intersection with CombineVariants and SelectVariants. Added integrationtests of CombineVariants with OMNI and HapMap that deal with the two ways to merge fitlered/unfiltered records at the same site.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5860 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 01:54:29 +00:00
653475ce12
Now finds the most likely configuration of genotypes given the genotype likelihoods and inheritance constraints. The parental genotypes are now phased as well (the alleles are ordered as A_transmitted|A_untransmitted). Rewrote the way the transmission probability is calculated. This will probably move into core soon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5859 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 01:35:40 +00:00
2efd807952
No more default callsets, they're now mandatory arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5858 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 21:56:43 +00:00
133712faec
Have a list of bam files but Picard updated their versions from v1 to v17 ? This script will update all your v* numbers for you.
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PS: don't hate Lua. :-)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5857 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 21:46:14 +00:00
4bfec4c55b
Reenabling E.coli ValidatingPileup with MV1994 realigned using the BWA/C bindings.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5856 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 21:32:53 +00:00
bc4305c956
Added memory limit parameter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5855 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 21:11:44 +00:00
c7f4674fe2
Great! Contracts is working. Fixing some misspecified ones.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5854 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 21:00:52 +00:00
833dff658a
Small script to do full variant annotation in parallel
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5853 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 20:33:20 +00:00
5dca1e4d2e
Make IntervalIntegrationTest aware of the new alignments in the MV1994.bam
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testset.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5852 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 19:59:47 +00:00
7ff5375493
Removing build-killing dependency on a private package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5851 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 18:13:15 +00:00
0b07373909
Incorporating old feedback from eric: @deprecated methods should not be @deprecated, but rather protected, and the test's package moved to where it can access those test methods.
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Also allows for the slightly more awesome name "MWUnitTest"
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5850 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 18:06:05 +00:00
f8f37a786d
Now emits much more informative filter names and includes all of other the proper VCF header details (filter description line, tag definitions, etc.). Currently rewriting the way the transmission probability is calculated. This is shaping up to be a lovely little piece of code...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5849 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 17:50:59 +00:00
912c6cdbfa
Moving this script out of playground while I figure out what's going on.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5848 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 17:48:44 +00:00
15dc632570
The U-value can be zero (edge case)
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z-value can not be NaN (and can't possibly be null)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5847 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 14:15:36 +00:00
3c31007da4
Stupid brackets. How did this even compile?
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5846 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 14:00:53 +00:00
480859db50
Contractified version of MannWhitneyU. Some behavior has been changed:
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- Running a test when there are no observations of at least one of the sets now breaks the MWU contract
+ MWU returns Pair(Double.NaN,Double.NaN) in these instances to maintain the contract of never returning null
+ No more Double.Infinity values will appear
- RankSumTests now probe the return values for NaNs, and don't annotate if they appear
- For small sets where the probability is calculated recursively, the z-value is now the inversion of the error function
and not the approximate z-value
- UG and Annotator integration tests updated to reflect changes
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5845 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 13:57:15 +00:00
b814f4bbd6
Contracts for HasGenomeLocation. BAQ iterator variables are all final. Contracts added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5844 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 02:21:59 +00:00
43057bd15c
Remove Param annotation and associated broken processing code, as this was never used in the codebase
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5843 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 02:21:15 +00:00
d005c4bf09
GenomeLocProcessingTracker was using SimpleTimer in a non-thread safe way. No longer providing an interface to time parallel operations. Now issues warning if someone enables distributed GATK, as this is considered an unstable, experimental engine feature.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5842 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 02:10:27 +00:00
a18b0152df
Contracts for SimpleTimer, as well as UnitTests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5841 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-22 19:45:31 +00:00
depristo
hanna
kshakir
fromer
corin
delangel
ebanks
kiran
carneiro
chartl