4014a8a674
A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.
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Thanks!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3135 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 06:14:15 +00:00
e148a3ac61
added the ability to create interval lists directly from a ROD, using the command line arg '-BTI' (long name '--rodToIntervalTrackName'). The parameter to this arg is the name of the ROD track, which must be a track name specified in the -B option.
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Using this feature, sites covered by the target ROD will be iterated over. This list of intevals generated is merged with any intervals from the -L and -XL args, and the Walker is run over the resulting merged list.
WARNING: for very large ROD's this can be costly. Consider this experimental for now.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3134 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 05:14:41 +00:00
20cc2a85a4
removed the hashmap from Genotype Concordance, moved it into a table
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3133 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 21:24:48 +00:00
e55f27b3b1
forgot a file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3132 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 20:51:13 +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
918b746798
More detailed validation output. Fixes for genotyping overflow -- these are temporary and need to be properly resolved
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3129 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 16:38:28 +00:00
e7dad728df
Trivial output changes for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3128 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 14:47:43 +00:00
058e7d3d12
Bug fix for Gregory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3127 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 00:21:35 +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
60c227d67f
Added new VE2 module to create a plot of titv ratio by variant quality score
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3125 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-06 15:19:27 +00:00
3530ef5a41
Explicit type cast fixed in order to work with new ROD implementation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3124 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-06 15:02:56 +00:00
2d002c56c3
Added histogram of variant quality scores broken out by true positive and false positive calls to the GenotypeConcordance module of VariantEval2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3123 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-06 13:48:31 +00:00
12e4f88ca7
a little bit more clean-up
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3122 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-05 20:49:06 +00:00
df7e7921ce
removing some unused code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3121 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-05 19:30:08 +00:00
56eb15f91f
Error checking for bad input (thanks, Aaron).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3120 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-04 03:17:01 +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
8017fb123f
changed the depth of coverage walkers class name, and added a dependency in the packaging system so that RODs will all get imported.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3116 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-02 20:55:19 +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
d7880ef7ad
Forgot to uncomment the AlignerIntegrationTest before committing. And yes, matt, commenting it out is, in fact, easier than just setting my classpath.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3110 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 17:17:16 +00:00
f7d1b8f5de
CoverageStatistics has now replaced DepthOfCoverage -- old DoC is in the archive.
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Also, I can't be bothered to fix the spelling of "oldepthofcoverage" to contain the necessary number of D's. Be content that it does, however, contain the requisite number of O's.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3109 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 16:27:23 +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
c3c6e632d1
support for two new VCF header info field value-types, Flag (for fields that are just boolean truths), and Character (for single charatcer info fields).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3105 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 03:11:32 +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
4fcee248f9
For Kristian: functions which, given a read, can uniquely identify the BAM file storing that read.
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Introducing this into the pile of code which peeks under the covers of the SAMDataSource in the hopes
that this function can help to replace the others and provide a single path for crosstalk.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3103 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-31 20:46:44 +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
b60197ae10
Another round of cleanup and simplification in Picard -- Picard's unit tests
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are now passing for my branch.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3100 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-31 01:02:59 +00:00
40f8e7644c
Better, multi-haplotype aware haplotype scores. Looking very good now, seems to be vastly better at dealing with incorrect calls in deep and low pass data. Almost ready for use
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3099 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 23:57:36 +00:00
f992f51a3b
Deleting incorrect sampling genotype likelihoods from the codebase
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3098 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 23:56:35 +00:00
b9d3fc3fbb
Now checks if the i-th element of the FiltrationContext[] is null before trying to access it. This seems to happen occassionally at the very end of a VCF file... the array will be 6 elements long, but the last element will actually be null.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3097 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 22:40:17 +00:00
400684542c
Revisions to take into account finalization of Picard patch: naming changes, better definition
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of public interfaces. This won't be the last Picard patch, but it should be the last big one.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3096 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 19:28:14 +00:00
b00d2bf2bc
fixing an annotation that was breaking the error log output system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3095 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 15:34:04 +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
babb9fb825
snp cluster filter should ignore ref calls when determining the clusters
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3093 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 17:57:33 +00:00
24461a2503
Let's *not* import classes that no longer exist. How my own ant test compiled is beyond me.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3091 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 13:59:01 +00:00
dc802aa26f
Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3090 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 13:32:00 +00:00
1e8b3ca6ba
Fare thee well, oh LocusWindowTraversal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3089 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 13:17:26 +00:00
8ea98faf47
Deleting the pooled calcluation model -- no longer supported.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3088 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 11:44:27 +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
a45ac220aa
Removing unnecessary printing routines
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3086 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-28 22:34:54 +00:00
b8ab74a6dc
Minor useful changes to BaseUtils and MathUtils to support a new haplotype score annotation that determines to the two most likely haplotypes over an interval and scores variants by their consistency with a diploid model. Appears to be useful.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3085 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-28 21:45:22 +00:00
e9e53f68ab
Filter lists can now end with .list or .txt.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3084 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-27 17:41:24 +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
391e5843e4
If the annotation engine has not been supplied, don't try to annotate anything.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3081 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-26 20:52:21 +00:00
8048b709a0
Selects a single sample on which to operate.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3080 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-26 20:50:58 +00:00
aaron
depristo
ebanks
rpoplin
asivache
weisburd
chartl
hanna
bthomas
kiran
kshakir