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Author SHA1 Message Date
ebanks ac9dc0b4b4 Removing VariantEval (v1); everyone should be using VE2 now. Docs coming ASAP. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3177 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 19:53:02 +00:00
ebanks 3330e254a9 Standardize the dbsnp track name in preparation for case-sensitivity 
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
ebanks 5f7564bf0a Better naming of output columns 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3175 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 18:08:07 +00:00
aaron e682460c1f add a fix so that XL arguments won't cancel out -BTI arguments, fixed a bug for Ben where the ROD -> interval list conversion was throwing an exception, and some old code removal. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3174 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 16:31:43 +00:00
aaron 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. 
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
ebanks 04909fa6ad Removing arbitrary selects 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3169 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 17:46:39 +00:00
ebanks f1189bac5a Bug fix: final map call wasn't being triggered (because we returned when ref==null before applying update0) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3168 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 16:58:55 +00:00
weisburd b930dc52a5 Integration test for GenomicAnnotator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3167 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 14:43:25 +00:00
weisburd c0f4695902 Improved handling of haplotypeReference and haplotypeAlternate columns. Added haplotypeStrand column. Improved handling of empty fields in data files. 
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
weisburd 74ec72d1ac Added AnnotatorROD - the TabularROD format specific to GenomicAnnotator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3164 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 14:39:50 +00:00
weisburd 77a6608784 Changed a variable name 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3163 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 14:38:18 +00:00
weisburd 7b8056099c Fixed 'N' reference-base handling, changed some comments, var names 
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
ebanks dde092fb61 Added the ability in VE2 to select which eval modules to run, so that you aren't forced to use all of them. You can use --list to list all of the possible modules to run. 
Heads up everyone: by default, *no* modules are run.  Please add "-all" to your scripts to maintain the previous behavior.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3161 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-13 22:15:58 +00:00
ebanks 0b575596f8 Fix for concordance: samples found only in truth no longer kill it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3160 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-13 21:33:49 +00:00
hanna 8573b0bc6f Refactoring intervals, separating the process of parsing interval lists, 
sorting and merging interval lists, and creating RODs from intervals.  This
gives Doug the ability to keep using our interval list parsing code when
sorting intervals on our behalf.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3159 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-13 15:50:38 +00:00
weisburd d0123956bc Modified comments. 
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
chartl 7b05091c04 DoC now does not require a -o argument. (Change for Matt) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3157 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-13 13:58:17 +00:00
ebanks e413882302 Generalizing the SequenomValidationConverter to be able to take in any arbitrary rod type (provided it can be converted to VariantContext). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3155 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-12 20:42:18 +00:00
hanna 14b8101d45 Error message fail. Failed to supply one of the valid interval file types. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3153 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-12 01:19:01 +00:00
hanna 60d54e69f3 Hackish fix to present a better error message if the file does not have the proper extension. Will work with Brett to come up with a better solution. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3152 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-12 01:11:27 +00:00
ebanks d06c7835d8 Adding performance tests for the indel realigner; should take ~3 hours. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3151 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-11 04:45:22 +00:00
ebanks 3434a61146 Don't trigger when ref=N (which can happen when a dbsnp track is provided) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3150 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-11 02:59:11 +00:00
ebanks 961ca05abc Removed outdated Sequenom rod and renamed HapMapGenotypeROD to HapMapROD. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3149 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-11 01:43:07 +00:00
ebanks fa01876255 UnifiedGenotyper performance tests (WG, WEx); currently takes just over an hour. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3148 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 19:42:29 +00:00
ebanks 0cc6d0fbbb One more quick memory improvement: reuse Alleles in a given context instead of creating new ones for each sample (duh). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3147 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 18:48:36 +00:00
rpoplin c2a37e4b5c Variant Quality Score modules in VariantEval2 no longer create huge lists which hold all of the quality scores encountered and instead cast the quality score to an integer and use hash tables. Bug fix for files in which all the quality scores are set to -1. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3146 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 18:36:06 +00:00
ebanks 71f38a9199 Adding performance tests for the recalibrator (Whole Genome and Whole Exome tests). 
Should take ~3 hours to run.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3145 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 18:30:59 +00:00
ebanks e73e6a4fb0 Significant memory improvements to plink code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3144 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 16:12:38 +00:00
rpoplin f1b1e70612 Bug fix for multisample calls in ApplyVariantClusterWalker 
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
ebanks 3f2455e346 Better error message as suggested by James P 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3141 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 05:52:53 +00:00
ebanks fba48b515a Heads up everyone: 
For consistency, these tools should be writing to the walker's output stream and no longer use the -vcf argument.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3140 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 05:37:25 +00:00
ebanks e286623f6f Use byte[] instead of String in an attempt to cut down on memory usage 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3139 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 05:32:54 +00:00
chartl 7025f5b51d Added an auxiliary table to DepthOfCoverage, which is the cumulative equivalent of the locus table (got tired of doing the calculation by hand). Also took care of a trailing tab in the per-locus output table. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3138 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-08 19:37:17 +00:00
aaron 9f6377f7fb added a performance test build option (for the upcoming performance test suite), and added a sample performance test for VariantEval. 
IMPORTANT: it was really redundant that we had -Dsingle and -Dsingleintegration to run single unit tests and integration tests, now you can just use -Dsingle to run a single test for performance, unit, and integration tests.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3136 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-08 15:37:15 +00:00
aaron 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. 
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
aaron 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. 
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
aaron 20cc2a85a4 removed the hashmap from Genotype Concordance, moved it into a table 
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
aaron e55f27b3b1 forgot a file 
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
aaron 9ca8e345fc by-by old junk. 
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
aaron 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. 
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
depristo 918b746798 More detailed validation output. Fixes for genotyping overflow -- these are temporary and need to be properly resolved 
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
ebanks e7dad728df Trivial output changes for consistency 
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
depristo 058e7d3d12 Bug fix for Gregory 
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
rpoplin 7b44e6bd55 ApplyVariantClusters now outputs interesting threshold points based on hitting the target novel TiTv 
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
rpoplin 60c227d67f Added new VE2 module to create a plot of titv ratio by variant quality score 
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
asivache 3530ef5a41 Explicit type cast fixed in order to work with new ROD implementation 
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
rpoplin 2d002c56c3 Added histogram of variant quality scores broken out by true positive and false positive calls to the GenotypeConcordance module of VariantEval2 
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
aaron 12e4f88ca7 a little bit more clean-up 
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
aaron df7e7921ce removing some unused code. 
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
ebanks 56eb15f91f Error checking for bad input (thanks, Aaron). 
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
weisburd 705b28e90d First attempt at implement record filtering based on special 'hap_ref', 'hap_alt' columns in the input files 
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
weisburd d78e7f6c0a Added documentation. 
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
aaron 8017fb123f changed the depth of coverage walkers class name, and added a dependency in the packaging system so that RODs will all get imported. 
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
weisburd 6b7b07f178 First checkin of GenomicAnnotator which annotates an input VCF file by pulling data in a generic way from an arbitrary set of TabularRODs. 
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
rpoplin 642c969896 reverting optimizer changes 
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
chartl d7880ef7ad Forgot to uncomment the AlignerIntegrationTest before committing. And yes, matt, commenting it out is, in fact, easier than just setting my classpath. 
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
chartl f7d1b8f5de CoverageStatistics has now replaced DepthOfCoverage -- old DoC is in the archive. 
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
aaron 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 
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
hanna d00bde22db Reverting one of Brett's changes that should not have been committed. Will 
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
bthomas b4f6f54502 Reorganizing the way interval arguments are processed 
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
aaron 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). 
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
aaron 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. 
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
hanna 4fcee248f9 For Kristian: functions which, given a read, can uniquely identify the BAM file storing that read. 
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
rpoplin d58fe70708 Correctly ignore filtered calls and indel calls in the truth sets 
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
hanna b60197ae10 Another round of cleanup and simplification in Picard -- Picard's unit tests 
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
depristo 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 
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
depristo f992f51a3b Deleting incorrect sampling genotype likelihoods from the codebase 
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
kiran 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. 
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
hanna 400684542c Revisions to take into account finalization of Picard patch: naming changes, better definition 
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
aaron b00d2bf2bc fixing an annotation that was breaking the error log output system. 
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
aaron 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. 
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
ebanks babb9fb825 snp cluster filter should ignore ref calls when determining the clusters 
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
chartl 24461a2503 Let's *not* import classes that no longer exist. How my own ant test compiled is beyond me. 
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
chartl dc802aa26f Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics 
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
ebanks 1e8b3ca6ba Fare thee well, oh LocusWindowTraversal. 
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
depristo 8ea98faf47 Deleting the pooled calcluation model -- no longer supported. 
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
hanna 85037ab13f Fix for Kiran's sharding issue (Invalid GZIP header). General cleanup of 
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
depristo a45ac220aa Removing unnecessary printing routines 
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
depristo 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. 
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
kshakir e9e53f68ab Filter lists can now end with .list or .txt. 
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
aaron 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 
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
kiran 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. 
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
kiran 391e5843e4 If the annotation engine has not been supplied, don't try to annotate anything. 
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
kiran 8048b709a0 Selects a single sample on which to operate. 
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
kshakir 20e3ba15ca Added an optional argument -rgbl --read_group_black_list to filter read groups. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3079 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-26 19:38:57 +00:00
ebanks 73a14a985b Moving VariantsToVCF to core. 
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
ebanks 14bf6923a8 HapMap-to-VCF now works fine within Variants-to-VCF. Added integration test for it and removed old code. 
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
hanna 78af6d5a40 New sharding system is going live again for on-the-fly merging. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3076 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-25 18:39:04 +00:00
hanna 46c14ec63f New, much less memory intensive implementation of BAM file sharding. Streams indices together with the expectation 
that bins will be present in the bin sparse array, which avoids the problem of having to hold the sparse bin array
stored in every BAM file index in memory at the same time.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3075 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-25 17:41:22 +00:00
ebanks 4398a8b370 Updated. Now uses VariantContext and is truly "variants" to vcf (i.e. not just GELI to vcf). 
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
ebanks 2373a4618f bug caused by a misprint: context != contexts 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3073 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-25 03:08:24 +00:00
ebanks 3176715c74 1. Alignability mask returns null when not available. 
2. --list now prints out the available classes/groups too.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3072 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 20:49:07 +00:00
rpoplin 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. 
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
ebanks 47e30aba92 Rods for reads hooked up into the cleaner 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3070 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 18:17:56 +00:00
aaron 5079f35e40 better method names for read based reference ordered data access. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3069 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 16:13:31 +00:00
ebanks 49117819f5 For the cleaner to clean, it must beat the entropy produced by the aligner (and not just the raw reads). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3068 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 15:21:58 +00:00
aaron 60dfba997b added some sample annotations to VariantEval2 analysis modules, and some changes to the report system. 
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
hanna 1f451e17e5 Changing preloaded index to only "preload" reference sequences on demand. 
Results in drastic lowering of startup cost when multiple BAM files are 
merged.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3066 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 22:02:28 +00:00
hanna 884a577013 Phase 2 of Picard patch refactoring: kill off SAMFileReader2/BAMFileReader2, merging the changes back into the base classes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3065 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 16:48:11 +00:00
aaron 7462a0b2d1 cleaned-up of VariantContextAdapter tests, fixed the double comparisons in equals() in RodGeliText (nice MathUtils.compareDoubles Kiran) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3064 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 15:18:30 +00:00
aaron a69b8555dd Geli to variant context. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3063 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 06:45:29 +00:00
aaron eafdd047f7 GLF to variant context. Added some methods in GLF to aid testing; and added a test that reads GLF, converts to VC, writes GLF and reads back to compare. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3062 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 03:43:25 +00:00
hanna 3767adb0bb Processing intervals as they stream in means much lower memory usage and 
quicker runtime.  Making change as minimal as possible to avoid conflicts
with BT's incoming patch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3061 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 22:04:45 +00:00
ebanks 0097106938 VariantFiltration can now filter specific samples. 
This is *NOT* an ideal implementation.  One day when we have lots of free time (or a greater desire), we will implement this correctly and sophisticatedly using all the power of JEXL.  For now, though, this will have to do.
Docs coming tonight.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3060 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 20:45:11 +00:00
asivache 543aefc3d7 Fixing the bug introduced with the earlier commit. When trimming locus to the current bases, we need to take into account expanded boundaries (for windowed reference traversals) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3059 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 19:20:34 +00:00
asivache ee1dc6092f Test updated. Now we do not throw an exception when locus interval is out of bounds, we just return silently a reference context trimmed to the current shard boundaries. New test checks for trimming. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3058 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 17:37:52 +00:00
asivache d2944461ef We also have to allow the window to be (partially) outside the bounds and trimming to the contig size is not enough (thanks to shards). Now we trim to the current bounds too (i.e. if the interval is not completely within current bounds, we create reference context that contains only bases from the overlap between the interval and the bounds). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3057 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 17:36:29 +00:00
asivache 9053406798 LocusReferenceView: If the locus a view is requested for spans beyond the reference contig ends, create the actual window bounded by contig ends (so that the locus will not be fully contained in the window!!). 
ReferenceContext: constructor does not throw an excepion anymore when locus is not fully contained inside the window. So now we can have a reference context associated with a locus such that the window/actual bases do not cover the whole locus. Scary. I am not sure I like this...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3056 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 15:59:15 +00:00
aaron 439c34ed38 clean-up before annotating VariantEval2 for output. 
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
depristo 076d21d394 Minor bug workaround in GenotypeConcordance module (see todo). General platform read filter. You can say -rl Platform illumina to remove all SLX reads 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3054 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 02:47:09 +00:00
hanna 6cd97b78ab An additional safety check to ensure that we only walk over coordinate-sorted 
data when doing locus traversals.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3053 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-21 23:31:45 +00:00
hanna b4b4e8d672 For Sarah Calvo: initial implementation of read pair traversal, for BAM files 
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
hanna c0eb5c27ea Lower memory support for merged sharding. Merged sharding is still not available. 
WARNING: If you update frequently, you might have to rm -rf ~/.ant/cache -- this is an unfortunate side effect of the way we
	 distribute picard-private.jar.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3050 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 22:03:47 +00:00
ebanks 4d4db7fe63 Renaming for consistency 
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
ebanks 4c4d048f14 Moving VariantFiltration over to use VariantContext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3048 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 18:35:23 +00:00
ebanks c88a2a3027 Fixing/cleaning up the vcf merge util 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3047 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 15:13:32 +00:00
rpoplin cdec84aa8f Bug fix for variant optimizer. Remember to close the PrintStreams it uses to output the cluster files. 
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
depristo d8ff552311 Support for EXPERIMENT sampling-based genotype likelihoods 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3044 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 13:19:40 +00:00
depristo 7b17bcd0af Refactoring a few useful routines for detecting mendelian violations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3043 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 13:19:01 +00:00
depristo 56092a0fc2 Slight cleanup for mathutils 
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
depristo b221ce94ce Still being tested trio-aware genotyper that calculates P(de novo) 
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
ebanks 03480c955c And now the UnifiedGenotyper can officially annotate genotype (FORMAT) fields too. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3039 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 04:58:37 +00:00
ebanks e757f6f078 Missing value for arbitrary format entries is empty string (need to revisit at some point, but it will require updating the VCF spec). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3038 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 03:56:27 +00:00
ebanks 0311980668 The VariantAnnotator can now officially annotate genotype (FORMAT) fields. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3037 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 03:30:14 +00:00
hanna 9b61d95d9c Khalid found an out-of-memory condition with the new sharding system when 
merging lots of BAMs, and the fix is taking longer than I thought.  Disable
experimental sharding when merging until the fix is ready.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3036 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 02:43:46 +00:00
ebanks b8e8852b4f Better interface for the Annotator in how it interacts with VariantContext. 
Also, added a proof of concept genotype-level annotation (not working yet, almost there).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3035 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 20:41:57 +00:00
hanna 96662d8d1b Moving from GATK dependencies on isolated classes checked into the GATK 
codebase to a dependency on a jar file compiled from my private picard branch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3034 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 17:43:42 +00:00
aaron 8a5f0b746e some cleanup for the output system. 
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
rpoplin c78fc23ec5 Minor updates to output of variant optimizer. 
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
ebanks 0247548400 Fixed one test and (temporarily) punted on another 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3030 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 06:22:48 +00:00
ebanks ee0e833616 Some significant changes to the annotator: 
1. Annotations can now be "decorated" with any arbitrary interface description - not just standard or experimental.
2. Users can now not only specify specific annotations to use, but also the interface names from #1.  Any number of them can be specified, e.g. -G Standard -G Experimental -A RankSumTest.
3. These same arguments can be used with the Unified Genotyper for when it calls into the Annotator.
4. There are now two types of annotations: those that are applied to the INFO field and those that are applied to specific genotypes (the FORMAT field) in the VCF (however, I haven't implemented any of these latter annotations just yet; coming soon).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3029 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 05:38:32 +00:00
rpoplin 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. 
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
hanna d9398dc347 Remove some of the restrictions on getStart() and getStop(); getStart() and getStop() 
now do the minimum validation rather than the more rigorous only-within-the-contig-bounds 
header validation.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3027 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 19:39:30 +00:00
aaron 182f1061ff Bamboo isn't picking up commits for some reason; updating a copyright to see if it'll get this commit. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3025 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 17:56:48 +00:00
ebanks 5e29d0c219 Be smarter about dealing with infinite quals for ref calls 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3024 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 17:35:23 +00:00
rpoplin 1bb4394aa9 Adding a skeleton for the second step of the variant optimization process. 
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
ebanks ded4ba8966 Let's make artificial reads that actually adhere to the specs... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3022 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 16:51:42 +00:00
bthomas 5b34bb9ab0 Adding three minor new features: 
+ -L all now walks over all intervals

+ if a -L argument is passed with a .list extension, and file does not exist, returns a \
File Not Found error instead of "bad interval" error. We plan to soon revisit interval \
lists and generate a concrete list of filenames, so this is likely temporary.

+ Error is thrown if the start position on an interval is higher number than the end position.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3021 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 16:24:10 +00:00
ebanks 4340601c26 -Pushed base quals back down into SAMRecord; if -OQ is used, the SAMRecord quals get updated automatically 
-Better integration test


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3020 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 16:00:10 +00:00
ebanks 76d14d17dc oops, need to update class names too 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3019 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 14:01:31 +00:00
ebanks 85a030069d renaming for consistency 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3018 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 14:00:28 +00:00
ebanks af5fd99444 Added filter for bad cigars (based on consecutive indels) - and cleaned up bad mates filter. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3017 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 13:53:42 +00:00
hanna 2cc040aa1c New sharding system is live. Disable with -ds. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3016 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 03:32:45 +00:00
ebanks 1fd909cdaf Fix for Kiran: -1 is a valid value for genotype qualities in VCF, so VariantContext shouldn't die. Cleaned up the relevant VCF code while I was in there. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3015 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 00:20:15 +00:00
hanna 849bd1f451 Set the eagerDecode flag in such a way that the binary data block in the BAM will always be considered dirty. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3014 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 22:01:23 +00:00
rpoplin 933823c8bc Removed the StingException when mkdir fails for Sendu in AnalyzeCovariates. Incremental updates to VariantOptimizer. 
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
hanna 2525ecaa43 Oops. Commented out some tests to improve performance and then checked in the commented out tests. Reverted. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3012 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 16:34:50 +00:00
hanna 59045ccb28 Filter,merge performs much better than merge,filter. Many thanks to Eric for checking in an integration test that so compellingly demonstrates this. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3011 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 16:23:37 +00:00
hanna 6dd5f192e7 Performance improvements for RODs in conjunction with new sharding system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3010 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 14:54:12 +00:00
kiran f20f78d77f Don't crash if the tracker is null. Reset the alternate alleles based on the alts present in the subset of samples. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3009 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 04:00:04 +00:00
aaron 10e76abbbc adding some VE2 report infrastructure; work-in-progress. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3008 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 03:57:42 +00:00
ebanks 586f87fa35 Quick fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3007 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 02:59:26 +00:00
ebanks 202231141c -Push the --use_original_qualities argument into the engine. 
-Check that base and qual strings are the same lengths
-Fix one more bug in the clipper.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3006 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 02:06:11 +00:00
ebanks 035d4170aa fix bug in read clipper: output bam can be null, so check for it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3005 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 18:49:26 +00:00
ebanks 411d25c8d1 -Integration tests for walkers that use original quals. 
-framework for pushing -OQ into GATK (not done)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3004 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 18:46:31 +00:00
aaron e365d308d4 add a new JEXLContext that lazy-evaluates JEXL expressions given the VariantContext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3003 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 16:00:55 +00:00
kcibul 9f519af06d new method to filter out overlapping PE reads 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3002 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 15:40:09 +00:00
hanna 45f70de6df Fixed bug that failed to reset an accumulator when crossing contig boundaries, 
meaning that in special cases of shallow coverage, an interval might get dropped.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2999 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 04:45:55 +00:00
ebanks 73d6167bd6 Fixing broken integration tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2998 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-14 23:18:49 +00:00
depristo 4dd7c5972c Unit tests for -XL arguments; expt. annotation calculating the GC content within 100 bp of the current SNP 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2997 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-14 21:08:14 +00:00
ebanks e367a50e9b Added genotype concordance module. Not at all finished, but needed to give something to Aaron to look at for help in printing the output nicely. 
Also misc cleanup and fixes (e.g. perform evalulation even when no comp tracks are provided).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2996 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-14 19:02:24 +00:00
aaron ecb59f5d0d removed old tests and old code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2995 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 22:57:01 +00:00
depristo e7eae9b61d High performance, correct implementation of -XL exclusion lists. Enjoy. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2994 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 22:39:20 +00:00
aaron 88a48821ea removed the dependence on removeRegion() in GenomeLocSortedSet 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2993 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 22:35:49 +00:00
depristo b39b5edca8 Bug fix in variant eval 2. Preliminary (slow and buggy) support for -XL exclude lists. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2991 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 19:23:12 +00:00
aaron 1eb5f97255 fixed dropping single base intervals from deleteRegion, moving onto performance fixes. 
(stop - start is length-1 on closed intervals, so we need to check greater than OR equals to zero)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2990 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 19:14:21 +00:00
hanna 7aa7a5f9b8 Bug fixes for edge cases and filtration in the earlier performance fixes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2989 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 04:46:08 +00:00
hanna 5e8654fcdc Oops! Introduced a performance bug in read interval sharding, when the new sharding system is available. Track more state to avoid this problem in the future. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2987 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 23:19:42 +00:00
asivache d804bdf210 New option: --maxReadsInRam . When using ON_DISK sorting option, the tool may still run out of memory in the regions of pathologically deep coverage because of the generous memory usage limit set in the underlying samtools' sorting sam writers. With this option, the user can lower the number of reads the writer keeps in memory before spilling them on disk. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2985 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 21:15:03 +00:00
aaron 661a043cef adding methods to get RODs by name or type in read traversals, performance improvements to RODs for Reads in general, and some more Tribble infrastructure. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2984 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 21:13:39 +00:00
depristo 18ba9929f9 notes for eric 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2983 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 20:34:54 +00:00
hanna cbd529d544 Better chopping up of data for ref walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2982 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 20:13:26 +00:00
hanna a7ba88e649 Rework the way the MicroScheduler handles locus shards to handle intervals that span shards 
with less memory consumption.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2981 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 18:40:31 +00:00
ebanks 4a05757a2a Fixed strand bias calculation because of -Infinity issues. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2980 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 16:05:51 +00:00
aaron dde9fd8a15 some rods-for-reads cleaning and performance improvements. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2979 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 22:54:58 +00:00
depristo 4f4555c80f PPV and Sensitivity added to validation tool output; support for arbitrary -sample arguments to subset variant contexts by sample 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2978 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 22:28:31 +00:00
ebanks 40d305bc7e Added test of Nway cleaning for Matt; thanks to Aaron for the help. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2977 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 21:00:41 +00:00
depristo 486bef9318 Support for validationRate calculation in variant eval 2; better error messages for failed genome loc parsing; tolerance to odd whitespace in plinkrod, and fix for monomorphic sites in vcf2variantcontext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2976 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 16:25:16 +00:00
ebanks c85ed1ce90 Plumbing is now in place to emit indel calls from the UnifiedGenotyper. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2975 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 04:30:12 +00:00
ebanks 5c35be39ef Now that extended events work for reference traversals, turn it off in the genotyper for non-indel models (thereby fixing busted integration tests). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2974 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 03:14:06 +00:00
ebanks 7ddd45d059 Hmm. I thought I removed this already. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2973 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 03:09:13 +00:00
ebanks 1a576525e9 misc improvements 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2972 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 03:00:28 +00:00
ebanks 6e855809e1 Renaming and moving relevant tools into a sequenom directory 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2971 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 02:31:10 +00:00
asivache c638c29eea In reference traversals, this view did not expect a possibility of TWO alignment contexts (base pileup followed by extended event pileup) associated with the same location. As the result, extended event pileups were silently skipped even when enabled in the traversal engine. Fixed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2970 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 22:18:44 +00:00
ebanks bc3761dc16 allow clipper to use original quals if requested 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2969 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 21:50:31 +00:00
ebanks f096a958d6 Initial commit for Andrey of plumbing for indels. Not finished - need to track down bug with him. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2967 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 19:13:01 +00:00
chartl 0a49dffa8f Row/Column names are now R-friendly 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2966 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 19:01:03 +00:00
ebanks 0e360ea8af Alleles now hash correctly. 
Special thanks to Matt & Aaron.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2965 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 18:09:44 +00:00
ebanks e5475a7ba9 re-enabling PlinkToVCF integration tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2964 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 17:35:49 +00:00
ebanks 5a20bf0e64 3 changes to UG which break integration tests: 
1. emit AA,AB,BB likelihoods in the FORMAT field for Mark
2. remove constraint that genotype alleles (in the GT field) need to be lexigraphically sorted.
3. Add bam file(s) used by genotyper to header for Kiran


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2963 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 17:16:47 +00:00
hanna cdce639bae Partially reclaim performance lost during integration test fixes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2961 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 12:36:11 +00:00
ebanks 9f3b99c11b Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system. 
Removing obsolete genotyping classes.
First stage of removing dependence on old Genotype class.
More changes to come.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2960 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 03:41:07 +00:00
hanna 02f48b6457 Fix bug that's been in the GATK for a very long time: update nReads (as well 
as nRecords), so that INFO logging doesn't say 'skipped 0 of 0 reads'.  While
I'm in there, update TraversalStatistics to store longs.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2959 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 22:44:54 +00:00
chartl bca9bdcc68 Add integration test for quartiles overflowing on interval reduce 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2957 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 16:18:45 +00:00
chartl 21bf8b4b93 Odd, what I saw on IntelliJ hadn't saved to sting before committing. Here's the actual change. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2956 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 15:54:41 +00:00
rpoplin fe8a8b9199 Hooked up both optimization models via command line arguments. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2955 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 14:49:59 +00:00
chartl cc6a714c09 Handle excess coverage in interval output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2954 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 14:40:05 +00:00
rpoplin ca2a0266dc Converting annotation values that are set to Double.Infinity 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2953 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 14:04:33 +00:00
rpoplin b42e0a398e Bug fix in variant optimizer for when there are more novel variants than known variants in the callset. Changing the magic numbers related to the starting sigma values for the gaussian clusters. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2952 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 13:02:08 +00:00
hanna e4360bac6a More comprehensive support when sharding for ref walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2951 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 11:25:20 +00:00