721e8cb679
VariantsToTable now supports wildcard captures. -F PREFIX* now captures all fields that begin with PREFIX, output as a comma-separated list of unique values. Added integration test for VariantsToTable since I find it so useful.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4706 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 18:54:59 +00:00
8cba86a69d
Trivial code organization for the haplotype score
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4703 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 12:32:55 +00:00
9f356b6cd0
Package all walkers in org/broadinstitute/sting/gatk/walkers directory in release.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4702 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 02:33:45 +00:00
90711d445c
Change the interface for RMDTrackBuilder, therefore always mandating the specification
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of a sequence dictionary and related info. This will hopefully eliminate the cases in
which the refseq track depends a sequence dictionary / contig parser that hasn't been
specified.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4700 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 19:00:17 +00:00
367cc9135f
Use VariantContext and Genotype accessor methods for attributes that will return null for unparseable data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4699 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 18:19:56 +00:00
2f3578182a
Added VERY preliminary version for merging refseq annotations as SNPs are merged
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4698 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:49:12 +00:00
e2f7f33ce7
Added getIntegerAttribute()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4697 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:33:07 +00:00
d86ab2becb
JEXL expressions now generate exceptions, not warnings. Tools should catch the runtime exception to handle correctly. Removed unncessary complexity from the JEXL contexts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4695 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:08:16 +00:00
539651de30
Initial version of Indel Statistics module for Variant Eval - not for general use yet, needs more verification and more work. Older IndelHistogram module will be obsolete with this new walker. Right now, for each sample (and for all samples), the following are computed:
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- Number of insertions
- Number of deletions
- Length distribution for indels.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4694 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 15:52:01 +00:00
01b721ab61
Passing ReviewedStingExceptions through the HMS.
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Added a @Hidden experimental argument -validate to VariantEval that allows external JEXL assertions that must evaluate to true will throw an exception.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4692 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-16 21:50:42 +00:00
f1b0f3bc49
Putting my changes from earlier in the day back in after someone (rhymes with 'Dark') trounced on them with his last commit...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4687 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-16 01:55:50 +00:00
ef2f6d90d2
VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4684 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 22:19:22 +00:00
5b83942cee
- Fix DepthOfCoverage so that, when it abuses the ROD system by instantiating a track in onTraversalDone, it also supplies the correct sequence dictionary and parser.
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- Changed RMDTrackBuilder to use SequenceDictionaryUtils.validateDictionaries for ref <-> ROD sequence dictionary validation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4683 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 20:34:04 +00:00
62be55376b
no longer useful
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4677 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 17:53:33 +00:00
35382468ee
Better error checking/output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4676 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 16:36:34 +00:00
7a3a464959
Finally, the logic is right
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4674 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 14:02:09 +00:00
8d66637fc2
Bug fix for VariantsToTable with filtered records
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4673 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 13:49:16 +00:00
d76b87d6e3
Useful debug file output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4672 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 13:36:52 +00:00
82f9327b5e
Throw the right exception
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4666 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-13 22:18:42 +00:00
44d0cb6cde
New version of cutting routines for VQSR. Old code removed. Working unit tests. Best practice with testng integration test (everyone look at it). Walker test now allows you to not specify no. input files, if it can infer input counts from MD5s
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4664 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-13 16:19:56 +00:00
673fa841a4
Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.
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Removed obsolete usages of PackageUtils with updated PluginManager.
Ported Queue interval utilities written in scala over to Sting's java IntervalUtils.
Added a very basic intergration test to ensure that the fullCallingPipeline.q compiles.
Added options to specify the temporary directories without having to use -Djava.io.tmpdir (useful during the above integration test).
While adding tempDir added options to specify the run directory from the command line, for example "-runDir v1".
Upgraded to scala 2.8.1 and updated calls to deprecated functions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4661 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 20:14:28 +00:00
988da428ae
Bug fix for old style tranches file. ApplyVariantCuts moved over, and passes integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4657 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 14:38:26 +00:00
c5f8c4dd0d
VariantEval test for tranches file, plus cutting over VE to use the generic Tranches framework
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4656 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 13:52:40 +00:00
69de3e51bf
Better precision for the calculated AF value. Now looks at the total number of samples to determine how much precision is necessary. Also, changing default min BQ used for calling in UGv2 to Q17.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4655 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 08:31:40 +00:00
ec83a4b765
Initial commit, without any tool changes, of a new infrastructure for determining tranches. This new version walker up from the lowest quality snps and determines Ti/Tv. This is marginally more stable than moving in the other direction when there are few novel variants (exomes). Can make a substantial difference in the size of the call set (10-20%). I'll hook it into the main system now. Includes an new class Tranche, isolated read/writing utilities that are now testing in TestVariantRecalibrator, which should be moved to UnitTest as soon as I can figure out how to do this on my mac.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4654 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 23:52:49 +00:00
ed6396ed43
No longer getting the inet, it seems to potentially hang the JVM
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4653 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 23:49:42 +00:00
dbde721dd0
Bug fix for filtered records
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4651 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 18:54:51 +00:00
698e5cf345
for GATK style codecs, make sure we fill in their GenomeLocParser from the RMDIndexer
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4650 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 18:44:15 +00:00
2e0296fef9
NWayOut logic slightly changed: 1) results.list file is gone; 2) now with -nWayOut one can specify either a) suffix to attach to every output file (i.e. cleaned reads from inputK.bam will be sent to inputK.suffix.bam) or b) *.map tab-separated file that must list <input_name> <output_name> mappings, one per line, for every input file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4645 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-10 20:32:16 +00:00
a1adfb91ce
And now @Hidden tags are really in place :-/
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4644 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-10 20:28:40 +00:00
68ce55148e
(pseudo-)genotyping functionality added: force-emits calls (including REF) at specified locations. Currently @Hidden for testing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4643 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-10 20:25:40 +00:00
8e36a07bea
Convert GenomeLocParser into an instance variable. This change is required
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for anything that needs to be simultaneously aware of multiple references, eg
Queue's interval sharding code, liftover support, distributed GATK etc.
GenomeLocParser instances must now be used to create/parse GenomeLocs.
GenomeLocParser instances are available in walkers by calling either
-getToolkit().getGenomeLocParser()
or
-refContext.getGenomeLocParser()
This is an intermediate change; GenomeLocParser will eventually be merged
with the reference, but we're not clear exactly how to do that yet. This
will become clearer when contig aliasing is implemented.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4642 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-10 17:59:50 +00:00
4759fdd2ac
V1 of read and variant simulator and assessor. SimulateReadsForVariants generates BAM and VCF with given combinations of variant and read properties. AssessSimulatedPerformance produces a table suitable for analysis in R
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4637 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-08 21:01:33 +00:00
97db593efb
making my last commit message actually true
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4636 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-07 18:26:23 +00:00
be499fc986
making the reference optional (the GATK will set it on the first run if it's not included), and setting the seq index if they do supply it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4635 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-07 18:15:31 +00:00
2a8c97a4a7
better error catching, as well as allowing for default index naming, <filename>.idx
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4633 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-06 19:12:19 +00:00
cb2e26a004
by request, an indexer tool to create Tribble style indexes outside of the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4632 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-06 18:59:06 +00:00
c9dbd8f80a
Bug fix for Tim: all point events must be treated equally
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4629 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-05 03:42:51 +00:00
913db5d1ab
Unfortunately when annotating sites with the UG the -G None option was wiping out the single annotations added by -A options
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4625 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-04 19:27:23 +00:00
816c86776e
Walker description was wrong and it was bothering me
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4624 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-04 02:17:09 +00:00
87f6738d4c
Deprecated
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4623 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-04 02:07:40 +00:00
42e9987e69
Bug fix to GenotypeConcordance. AC metrics get instantiated based on number of eval samples; if Comp has more samples, we can see AC indeces outside the bounds of the array.
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Bug fix to LiftoverVariants - no barfing at reference sites.
AlleleFrequencyComparison - local changes added to make sure parsing works properly
Added HammingDistance annotation. Mostly useless. But only mostly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4622 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-03 19:23:03 +00:00
3d27defe93
Fixed output stats (percentage denominator)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4621 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-03 18:47:06 +00:00
22d64f77ff
Added hidden --outputMultipleBaseCountsFile option to detect cases where a single read has more than one base at the same position
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4619 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-03 03:22:48 +00:00
a885ecf046
When merging MNPs, the phased flag and the phase quality (PQ) are determined simultaneously
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4613 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-02 14:44:26 +00:00
861ee3e37a
Changing testing framework from junit -> testng, for its enhanced configurability.
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Initial test to see how Bamboo will respond. More detailed email to follow.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4609 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 21:31:44 +00:00
fe3f78e1d3
make it full (absolute) path for the file names recorded in results.list
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4608 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 20:53:51 +00:00
2ac5e55130
typo
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4607 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 20:38:02 +00:00
0e6dd38936
In n-way-out mode, added printing names of all the output files into 'results.list' file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4606 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 20:37:38 +00:00
64599d1074
Added debugging message
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4605 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 19:51:42 +00:00
639ecdc931
Noted in comment that using a single sample in MergePhasedSegregatingAlternateAllelesVCFWriter does NOT update any of the INFO fields, though this could be changed in the future...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4604 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 19:02:52 +00:00
8439f0aa61
Check for VCFConstants.MISSING_VALUE_v4 when retrieving INFO fields and consider such values as non-existent
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4603 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 17:51:35 +00:00
aadd230636
N-Way-Out is back. Now uses SAMReadID to identify each read's source bam, so should be reliable. Interface is sort of ugly fo now: to generate output file names, .bam is stripped from input file names, then the value of -nWayOut argument is pasted on (and all the output files are written into the current dir).
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Unrelated change: in the sorted-target mode (when we read sorted target intervals one by on from a file), one can now specify multiple semicolon-separated interval files (all must be sorted). Not hugely useful probably, but makes --targetIntervals always process its values in exactly the same way, so we are consistent (it has been already taking ;-separated args in unsorted mode)
NwayIntervalMergingIterator: reads in multiple sorted GenomeLoc input streams (iterators) and presents them as a single sorted and merged stream
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4602 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-01 16:06:51 +00:00
23cb399a88
Reasonable first pass at a correct SB calculation. Simple utilities to support it. VariantsToTable no longer prints filtered sites by default. New non-standard variant eval module to print comp sites not present in eval (FN finder)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4601 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-31 12:41:52 +00:00
d492621122
The TraversalEngine's habit of hanging onto old ROD states seems to have a bad
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interaction with Tribble. In Tribble, keeping these references in memory until
the shard is flushed means keeping one 512K character buffer per object in
memory. Fixed by purging the reference to the object at the end of the
shard traversal.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4599 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-29 17:09:58 +00:00
1c056ea791
Users can now use VariantAnnotator to add annotations from one VCF to another. For example, if you want to annotate your target VCF with the AC field value from the rod bound to CEU1kg, you can specify -E CEU1kg.AC and records will be annotated with CEU1kg.AC=N when a record exists in that rod at the given position.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4598 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-29 16:38:31 +00:00
1b3fc8ddd2
Doing things too quickly is also naughty. Thanks, Andrey. Now, we're even.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4597 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-29 14:50:04 +00:00
58f7b4c595
Naughty use of assertions means that malformed records are not caught.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4596 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-29 14:41:38 +00:00
9a60e72364
Trivial change to LeftAlignVariants: make walker return number of aligned variants on map(), and print out the # of aligned variants at the end of the traversal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4595 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-29 02:03:36 +00:00
2f8057bf24
Cleanup for multithreading memory leak during integration tests...unregister MXBean at end
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of traversal to avoid holding a reference to the microscheduler, which holds a reference to
the engine, which in turn holds a reference to the walker, which itself holds a reference to
all the data aggregated during the course of the traversal.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4594 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-28 18:37:42 +00:00
fe3cfb067c
very minor cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4590 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-28 02:11:33 +00:00
cbce3e3c83
General support for both GL (log10) and PL (phred-scaled) genotype likelihoods. All walkers now use the Tribble GenotypeLikelihoods object for parsing VCFs with genotype likelihood fields. Please use GenotypeLikelihoods object from now on for seamless support for GL and PL tags. UGv2 now uses PL by default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4589 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-28 01:48:47 +00:00
15183ed778
Reduced header to single sample when useSingleSample arg is given (to prevent lots of pointless no-calls)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4588 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-27 23:02:10 +00:00
34538bf2b3
Added ability to focus only on a single sample and/or emit only merged records in MNP merger
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4587 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-27 20:41:05 +00:00
4c23b1fe9c
Get rid of the static cache of ArgumentTypeDescriptors by making them an integral part of the
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parsing engine. Hugely lowers our memory footprint in integrationtests, but not yet enough to
run Mark's new parallelized VariantEvalIntegrationTests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4585 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-27 19:44:55 +00:00
e112df20df
Use a sorting VCF writer because records can flip positions during left-alignment
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4583 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-27 06:33:03 +00:00
708e973911
Adding a walker to left-align indels in a VCF file (was able to reuse code from AlignmentUtils to do the hard part). The code correctly updates the alleles if they change. This makes it much easier to compare our indel calls to e.g. CG or dbSNP.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4582 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-27 06:08:26 +00:00
ec442086ec
Minor refactoring of the cleaner allows me to add a trivial walker that left aligns the indels present in reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4581 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-27 03:39:10 +00:00
ffc0ed2b32
Renamed getName() to getSource() in VariantContext to be more accurate
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4579 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-27 02:21:41 +00:00
52fc023d80
Added convenience methods to check/get the ID of the VariantContext
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4578 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-27 01:56:58 +00:00
a7af1a164b
Updated MNP merging to merge VC records if any sample has a haplotype of ALT-ALT, since this could possibly change annotations. Note that, besides the "interesting" case of an ALT-ALT MNP in a pair of HET sites, this could even occur if two records are hom-var (irrespective of using phasing). Note also that this procedure may generate more than one ALT allele.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4577 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-27 01:50:36 +00:00
e02aac0743
No longer print out 0 reads were filtered out... message when there were no reads scene at all
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4575 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-26 20:22:16 +00:00
b085648141
Parallelized VariantEval. Refactored output to support parallel output style. Minor improvements to testing framework to enable easy executeTestParallel to run -nt 1 and -nt 4 by default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4574 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-26 20:21:38 +00:00
071799453c
More complete fix to previous commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4571 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-25 20:47:37 +00:00
67a776d53c
Yikes! VariantEval was always loading genotypes unnecessarily when no sample list was provided because the order of the checks in the if statement wasn't optimal. This results in a massive performance penalty when running with many-sample VCFs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4570 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-25 20:30:23 +00:00
0d97394c4f
Add capability to liftover to do the right thing when sections of the genome are reverse complemented. This does not work for indels (we don't try to reverse complement) because we need to figure out what the hell to do about the fact that the 'base to the left' that we automatically add on will be wrong because the location of the indel actually changes when reverse complemented. Sheesh.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4569 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-25 20:03:03 +00:00
c357ec775a
Trivially phases any hom site (since it is always correct to continue the previous haplotypes by appending the same allele onto both haplotypes)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4568 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-25 16:58:41 +00:00
da64183854
Fix for the case of the truth VCF file having multiple SNPs at the same locus.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4567 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-25 15:04:50 +00:00
3039c0de3c
Retire old ROD syntax.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4564 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-22 23:52:11 +00:00
78e71c4167
Fisher exact makes a return. Seems to be working properly. Current tagged as a work in progress. Needs to take the filtered context to be truly correct.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4561 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-22 20:35:44 +00:00
f06f955e06
Added count of number of mergeable records (within specified distance cutoff)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4560 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-22 20:11:15 +00:00
78b4a1c240
VariantsToTable now supports the virtual TRANSITION field
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4558 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-22 19:53:46 +00:00
e6d61197e6
Disable OTF indexing when writing indices for temporary VCFs when running
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with -nt option. When last I checked in, Ryan was seeing a ~25% speedup
per shard by not indexing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4556 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-22 17:40:37 +00:00
e6b008f87c
Fixed >= vs. > test leading to failure to tolerate dynamic indexes that are created at *exactly* the instant the output VCF is closed too
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4555 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-22 16:11:14 +00:00
72c5b75460
Tribble exceptions can be generated outside of the normal codec parsing code because we now lazy load the VCF genotype fields. I'm not sure how else to account for this (to make sure they show up as user errors and not GATK system errors) besides catching them here.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4554 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-22 15:22:17 +00:00
c0b4317311
Er, here's the right fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4552 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-22 15:08:25 +00:00
9f76aed515
Fix for IDs 5zP7jJeffK2sdPH1BH4JBVSrQztVEDKP and nX0cuBjoqBW4NQFpM6dE13KpkCuYFpZu
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4550 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-22 14:05:27 +00:00
d4feb99d9a
For parallel ROD traversals, simplified reference sharding. Will replace
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with a more sensible strategy for sharding w/o BAMs at some point after
ASHG.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4549 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-22 05:08:15 +00:00
60f88866dd
Uses VCFConstants instead of hard-coded constants
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4547 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-21 19:49:01 +00:00
883b8ff80e
Removed flush() method from VCFWriter interface; added takeOwnershipOfInner parameter in constructor of wrapper VCFWriters to designate if the Writer should close the inner Writer it receives on construction
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4546 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-21 19:48:00 +00:00
1ea43be976
Removed flush() method from VCFWriter interface
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4545 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-21 19:46:42 +00:00
3566ad2146
Wrong if statement.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4544 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-21 17:37:45 +00:00
bf17f92b64
Do not look for samples in dbsnp binding
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4543 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-21 17:36:38 +00:00
cf9c9ae241
Three important updates for Dindel genotyper:
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a) Fix it up because it broke with a recent checkin to annotate vcf with unfiltered depth.
b) Printout of ref/alt alleles in output vcf was incorrect because the start/stop positions of associated GenomeLoc were incorrectly computed in case of a deletion.
c) Redid Beagle input/output walkers as not assume that ref was a single base, not to assume that variant was a vcf and generalized it to be indel-capable, so now the Beagle walkers can be used for indels as well.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4541 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-21 16:00:16 +00:00
8f38ebf98e
Throw a user exception when using the clustered SNP filter in the presence of ref calls. It's unfortunate, but until we get a windowed ROD context this is just too much of a headache to support.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4537 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-21 02:44:10 +00:00
91049269c2
Optimizations across the board, with help from Guillermo, Matt, and JProfiler. Too tired to give details now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4535 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-20 20:47:41 +00:00
f76865abbc
ReadBackedPhasing now uses a SortedVCFWriter to simplify, and has the ability to merge phased SNPs into MNPs on the fly [turned off by default]; MergeSegregatingPolymorphismsWalker can also do this as a post-processing step; Integration tests for MergeSegregatingPolymorphismsWalker were also added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4534 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-20 20:27:10 +00:00
e8079399ac
Added flush() method to VCFWriters
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4533 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-20 20:23:22 +00:00
00726b6c4b
Added mergeIntoMNPs to merge successive VCF records into a single MNP VCF [if possible]
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4532 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-20 19:40:26 +00:00
4f77581087
More optimizations for HaplotypeScore: pulling final constants out of loops
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4530 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-20 17:40:57 +00:00
depristo
hanna
fromer
delangel
kshakir
ebanks
aaron
asivache
rpoplin
chartl