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Author SHA1 Message Date
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