80c4f88a72
removing the Variation interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3216 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 18:56:45 +00:00
f4977965b6
Removing debug statements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3208 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 16:22:40 +00:00
124b7a2a58
Moved ApplyVariantClusters over to VariationContext
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3207 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 16:20:25 +00:00
c1e53d407d
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
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unicode quote characters embedded in it. These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset. Fixed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 15:26:32 +00:00
b5f6f54968
Almost done removing any trace of the old Variation and Genotype interfaces.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3202 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 14:52:15 +00:00
1bc26f69e9
An attempt to cleanup the Utils directory. Email to follow.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 23:00:08 +00:00
d73c63a99a
Redoing the conversion to VariantContext: instead of walkers passing in a ref allele, they pass in the ref context and the adaptors create the allele. This is the right way of doing it.
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Also, adding some more useful integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3194 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 05:47:17 +00:00
131703d9db
more clean-up: moving AlleleBalanceInspector to archive.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3192 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 20:53:33 +00:00
8c32bb8f0a
Complete the move over to VariantContext so that we can remove dependence on Variation (in the VCF code)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3190 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 19:41:42 +00:00
e11ca74eb5
removing some outdated ROD classes (PooledEMSNPROD and SangerSNPROD), removing an out-of-date interface (VariantBackedByBenotype), and moving AnalyzeAnnotationWalker over to VariationContext.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3188 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 18:59:29 +00:00
f4673efd2f
Moving to archive as it's no longer supported
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3182 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 22:10:42 +00:00
e702bea99f
Moving VE2 to core; calling it "VariantEval" (one more checkin coming)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3179 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 20:25:47 +00:00
3330e254a9
Standardize the dbsnp track name in preparation for case-sensitivity
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3176 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 19:41:57 +00:00
b54031fc86
adding an experimental format to VariantEval2, which when you source() from R, imports all VE2 output as individual tables with appropriate row and column names. More testing and feedback needed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3172 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 06:09:27 +00:00
c0f4695902
Improved handling of haplotypeReference and haplotypeAlternate columns. Added haplotypeStrand column. Improved handling of empty fields in data files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3166 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:42:19 +00:00
7b8056099c
Fixed 'N' reference-base handling, changed some comments, var names
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3162 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:37:25 +00:00
d0123956bc
Modified comments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3158 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 15:41:59 +00:00
f1b1e70612
Bug fix for multisample calls in ApplyVariantClusterWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3142 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 12:01:15 +00:00
9ca8e345fc
by-by old junk.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3131 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 20:41:48 +00:00
8fd59c8823
Modified the report system based on Ryan's feedback: tables are now created independently to avoid the permutation problem when they were all compressed in rows, and removed our dependency on FreeMarker. The Grep format stays the same.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3130 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 20:39:55 +00:00
7b44e6bd55
ApplyVariantClusters now outputs interesting threshold points based on hitting the target novel TiTv
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3126 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-06 19:47:29 +00:00
705b28e90d
First attempt at implement record filtering based on special 'hap_ref', 'hap_alt' columns in the input files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3118 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 21:52:26 +00:00
d78e7f6c0a
Added documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3117 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 21:51:28 +00:00
6b7b07f178
First checkin of GenomicAnnotator which annotates an input VCF file by pulling data in a generic way from an arbitrary set of TabularRODs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3114 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 17:49:42 +00:00
642c969896
reverting optimizer changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3112 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 16:59:13 +00:00
585cc880a2
changed jexl expressions to jexl names in the VariantEval2 output, fixed integration test, and fixed a problem where a line was getting dropped in CSV output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3108 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 16:23:14 +00:00
d00bde22db
Reverting one of Brett's changes that should not have been committed. Will
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address with Brett separately.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3107 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 16:10:46 +00:00
b4f6f54502
Reorganizing the way interval arguments are processed
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Most of the changes occur in GenomeAnalysisEngine.java and GenomeLocParser.java:
-- parseIntervalRegion and parseGenomeLocs combined into parseIntervalArguments
-- initializeIntervals modified
-- some helper functions deprecated for cleanliness
Includes new set of unit tests, GenomeAnalysisEngineTest.java
New restrictions:
-- all interval arguments are now checked to be on the reference contig
-- all interval files must have one of the following extensions: .picard, .bed, .list, .intervals, .interval_list
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3106 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 12:47:48 +00:00
3d3d19a6a7
the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date.
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a caveat: for anyone asking for all of the ROD's back from the RefMetaDataTracker (if your not using the facilities to get the track by name), you'll now be getting back a collection of GATKFeature objects. This object will contain the track name, and a method for getting the underlying object (getUnderlyingObject()), which will be the traditional RodVCF, rodDbSNP, etc. This layer is needed so we can integrate Tribble tracks (which don't natively have names). Calls that ask for RODs by name will still get back the traditional reference ordered data objects (RodVCF, rodDbSNP, etc).
Sorry for the inconvenience! More changes to come, but this is by far the largest (as has the greatest effect on end users).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3104 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-31 22:39:56 +00:00
d58fe70708
Correctly ignore filtered calls and indel calls in the truth sets
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3101 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-31 14:33:01 +00:00
a6e8687d71
implementing a clean way to import the template files into the GATK jar (they should not always get bundled). All further resources should be added to the gatk.resources path id in the build script.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3094 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 04:20:19 +00:00
85037ab13f
Fix for Kiran's sharding issue (Invalid GZIP header). General cleanup of
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Picard patch, including move of some of the Picard private classes we use to Picard public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3087 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 03:21:27 +00:00
074ec77dcc
First go of the new output system for VE2. There are three different report types supported right now (Table, Grep, CSV), which can be
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specified with the reportType command line option in VE2.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3083 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-27 03:59:32 +00:00
85f4f66180
Updated to use VariantContext. Output has been reformatted: variant and genotype concordance are emitted for every coverage level per variant. If the requested sampling level is higher than what's available, the maximum available coverage at that locus is used. This makes it much easier to make plots indicating the percentage of comparison callset recovered at a certain sampling depth.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3082 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-26 21:02:43 +00:00
73a14a985b
Moving VariantsToVCF to core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3078 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-26 18:55:12 +00:00
14bf6923a8
HapMap-to-VCF now works fine within Variants-to-VCF. Added integration test for it and removed old code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3077 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-26 18:34:59 +00:00
4398a8b370
Updated. Now uses VariantContext and is truly "variants" to vcf (i.e. not just GELI to vcf).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3074 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-25 04:53:31 +00:00
06a212e612
Adding VariantConcordanceROCCurveWalker to create ROC curves comparing concordance between optimized call sets and validation truth sets in VCF format in order to evaluate performance of variant optimizer independently of achieving a particular novel ti/tv ratio. Added option to ignore only the specified filters in the input call sets via --ignore_filter <String>. Added option to provide a prior estimate of error for known snps via --known_prior <qual>. The het and hom calls are clustered independently. Infrastructure in place to use titv of known snps to inform p(true) of novel snps. Tweaked protection against overfitting based on suggestions from several people. Minor edits to AnalyzeAnnotations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3071 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-24 19:43:10 +00:00
60dfba997b
added some sample annotations to VariantEval2 analysis modules, and some changes to the report system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3067 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-24 05:40:10 +00:00
439c34ed38
clean-up before annotating VariantEval2 for output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3055 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-22 07:39:20 +00:00
b4b4e8d672
For Sarah Calvo: initial implementation of read pair traversal, for BAM files
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sorted by read name.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3052 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-21 23:22:25 +00:00
4d4db7fe63
Renaming for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3049 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 18:45:01 +00:00
cdec84aa8f
Bug fix for variant optimizer. Remember to close the PrintStreams it uses to output the cluster files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3046 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 15:07:32 +00:00
56092a0fc2
Slight cleanup for mathutils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3042 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 13:18:08 +00:00
b221ce94ce
Still being tested trio-aware genotyper that calculates P(de novo)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3041 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 13:11:39 +00:00
8a5f0b746e
some cleanup for the output system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3032 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-18 12:54:39 +00:00
c78fc23ec5
Minor updates to output of variant optimizer.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3031 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-18 12:46:47 +00:00
58a31bab6a
Variant optimizer now outputs VCF files via ApplyVariantClustersWalker. Documentation to be added to the wiki. It is ready to be used by other people but only with great caution.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3028 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-17 20:41:42 +00:00
1bb4394aa9
Adding a skeleton for the second step of the variant optimization process.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3023 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-17 17:03:40 +00:00
933823c8bc
Removed the StingException when mkdir fails for Sendu in AnalyzeCovariates. Incremental updates to VariantOptimizer.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3013 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-16 19:45:02 +00:00
aaron
rpoplin
hanna
ebanks
weisburd
bthomas
kiran
depristo