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973 Commits (2520889cb35d09acf8313868c542bdfd98b9ae80)

Author SHA1 Message Date
kiran ff6877a15e Added a forgotten column label 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2622 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-18 01:00:52 +00:00
kiran dd6d5aadf9 Computes empirical confusion matrices, optionally with up to five bases of preceding context 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2621 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-18 00:55:12 +00:00
depristo d0af7f6c7b Now analyzes filtered SNP like all, novel subsets; support for selecting a single sample to analyze from a multi-sample VCF, support for trivial selection of records with INFO field key/value pair. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2613 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-16 20:22:04 +00:00
depristo 8ae8e120f8 New annotateUnion operation -- provides clearer annotations on where a call came from when unioning two VCF call sets 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2612 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-16 20:20:37 +00:00
rpoplin 4de7d6a59b Initial checkin of skeleton code for AnalyzeAnnotations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2605 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 21:52:34 +00:00
mmelgar 3063224446 SecondaryBaseTransitionTableWalker now breaks by genotype and read group, is javadoc annotated, and is compatible with ReadBackedPileup's methods. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2603 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 21:43:39 +00:00
aaron db9570ae29 Looks bigger than it is: 
* Moved GATKArgumentCollection into gatk.arguments folder to clean up the main folder, also added some associated argument classes (most of the changes).
* Added code the argument parsing system for default enums, we needed this so we could preserve the current unsafe flag, and at the same time allow finer grained control of unsafe operations.  You can now specify:

"-U" (for all unsafe operations), "-U ALLOW_UNINDEXED_BAM" (only allow unindexed BAMs), "-U NO_READ_ORDER_VERIFICATION", etc.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2586 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 00:14:35 +00:00
kiran 04fdbbfa65 This is the beginning of a new version of VariantEval that can cut VCF files up in a variety of ways with JEXL expressions, select one sample out of a multi-sample VCF, and can load analysis modules dynamically. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2584 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-14 17:45:58 +00:00
chartl 424d1b57f7 Sequenom to VCF now allows user to specify filters for QC, and they will appear in the filter field of the output VCF 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2577 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 23:22:37 +00:00
chartl 6d1107a4ed Update to SequenomToVCF 
Output changing slightly so integration test disabled temporarily



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2571 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 15:32:05 +00:00
ebanks 040fdfee61 Cleaned up the interface to VCFRecord. It's now possible (and easy) to create records and then write them with a VCFWriter. 
I've updated HapMap2VCF to use the new interface; Chris agreed to take care of Sequenom2VCF.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2558 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-11 21:42:12 +00:00
chartl dfa3c3b875 Added: 
SequenomToVCF - Takes a sequenom ped file and converts it to a VCF file with the proper metrics for QC. It's currently a rough draft,
but is working as expected on a test ped file, which is included as an integration test.

Modified:

VCFGenotypeCall -- added a cloneCall() method that returns a clone of the call

Hapmap2VCF -- removed a VCFGenotypeCall object that gets instantiated and modified but never used
(caused me all kinds of confusion when I was basing SequenomToVCF off of it)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2554 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-11 17:17:21 +00:00
ebanks 971834ca90 Added a walker to the vcf tools compilation: one that combines vcf records. Both merges and unions are supported (see documentation... when it gets written this week). 
Also, moved some code that pulls samples out of rods from VCFUtils into SampleUtils.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2552 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-10 06:45:11 +00:00
ebanks b643a513bb Minor interface change for VCFGenotypeRecord. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2537 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 16:48:09 +00:00
andrewk 431e9c2c8b Add dbSNP ID to VCF output records 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2536 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 15:30:04 +00:00
depristo 7215526810 Fix to isReference() in VCFRecord. Change to VariantCounter to correctly counter only non-genotype variants, as well as update to VariantEvalWalker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2531 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 00:03:29 +00:00
andrewk 6c4ac9e663 Updated HapMap2VCF to use the VCFGenotypeWriterAdapter interface; fixed bug in VCFParameters that affects VariantsToVCF and HapMap2VCF when reference is lower-cased; added integration test for HapMap2VCF that checks for the lower-case issue by testing against Hg18 region that has lower-cased bases 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2530 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 21:27:11 +00:00
aaron 576594eda2 clean-up of the GATK paper genotyper, and better output formatting for the simple call format we emit. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2529 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 20:54:56 +00:00
depristo 1e462419da trivial code restructuing, and commented out failed attempt to support sample selection with VCF. VariantEval2 go go go 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2516 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 15:04:27 +00:00
depristo 34519b3e3b Better printing support for false positives and false negatives in concordance tables 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2514 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 15:02:40 +00:00
depristo 21a50eedb5 Simple extension to VariantEval: --includeFilteredRecords will now keep filtered VCF records so you can see what the entire call set looks like. Looking forward to VariantEval v2 from Kiran. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2506 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 12:59:09 +00:00
depristo 8d13597a27 Temporary command-line support to enable rod walkers, if you know what you are doing this is safe. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2505 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 12:15:36 +00:00
depristo 87e863b48d Removed used routines in duputils; duplicatequals to archive; docs for new duplicate traversal code; general code cleanup; bug fixes for combineduplicates; integration tests for combine duplicates walker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2468 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 19:46:29 +00:00
depristo 29f94119d1 Fixes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2466 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 18:08:41 +00:00
depristo fcc80e8632 Completely rewritten duplicate traversal, more free of bugs, with integration tests for count duplicates walker validated on a TCGA hybrid capture lane. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2458 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 23:56:49 +00:00
andrewk 57516582c2 Converter from HapMap chip genotype data to VCF added; HapMapGenotypeROD adjusted to not convert from Hg18 to b36 formatting of contigs 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2447 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 01:36:08 +00:00
kiran 164a94a3d0 Modified the walker documentation so that the stray punctuation wouldn't cause the GATK to stop parsing the help documenation early (aka I changed one word). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2429 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-22 20:50:01 +00:00
kiran 4ee6a478e3 Creates a table of reference allele percentage and alternate allele percentage at Hapmap-chip sites in a BAM file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2428 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-22 20:43:44 +00:00
ebanks a5f75cbfd4 The previous commit broke the build, so this is a temporary patch to get it to compile. ConcordanceTruthTable should use enums (esp. now that all of the concordance variables need to be public), but VariantEval will need to be rewritten soon anyways so I'll just push it off until then. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2413 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-20 02:34:41 +00:00
depristo ee8bcdc61d PooledConcordance calculations have been reformatted and bugs fixed. Now properly handles monomorphic sites. Also works with -G option now, correctly 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2412 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-19 23:22:36 +00:00
depristo 9bf2d12c64 Misc. improvements to the LMW code. Support for emitting all sites, regardless of genotype. Min and max quality scores. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2411 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-19 23:20:57 +00:00
aaron c39675d2c1 VCFTool.java got left off of the last commit 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2407 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 21:33:53 +00:00
ebanks 4ea31fd949 Pushed header initialization out of the GenotypeWriter constructors and into a writeHeader method, in preparation for parallelization. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2406 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 19:16:41 +00:00
jmaguire 98839193b7 compatibility with VCF lib's switch to GenomeLoc. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2397 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 00:52:48 +00:00
jmaguire 8787dd4c5e Various and sundry additions to VCF tools. Some useful to the general public, some one-offs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2396 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 00:35:45 +00:00
andrewk 36875fca89 Update documentation in the new help system 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2380 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-16 21:33:12 +00:00
sjia 2deae95df9 Updated documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2370 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 21:31:47 +00:00
hanna 555976d575 One more walker with formatting to fix. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2369 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 21:23:13 +00:00
hanna cf46472419 Fix up Sherman's new docs in compliance with javadoc specs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2368 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 21:20:38 +00:00
sjia df79ed8db1 Updated documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2367 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 20:53:41 +00:00
sjia a80a5f1036 Updated documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2366 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 20:52:08 +00:00
sjia 18f61d2586 Updated documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2365 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 20:45:19 +00:00
sjia 5974c42468 Updated documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2364 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 20:41:35 +00:00
sjia d8cfd707bc Updated documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2363 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 20:35:18 +00:00
sjia 4322beeb35 Updated documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2362 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 20:33:38 +00:00
sjia 4148991d81 Now also encodes amino acids, includes documentation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2361 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 20:26:56 +00:00
depristo a810586418 Check-in without javadoc = smackdown 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2359 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 15:32:39 +00:00
depristo 0d2a761460 Bugfix for minBaseQuality to ignore deletion reads. LocusMismatch walker now allows us to skip every nths eligable site 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2357 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 14:38:39 +00:00
depristo faa638532a Correct location 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2353 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 02:42:21 +00:00
depristo 1da97ebb85 Walker for calculating non-independent base errors, v1. Will be moved to somewhere not in core 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2352 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 02:40:15 +00:00
chartl b42fc905e8 Added - new tests (Hapmap was re-added) 
Modified - Hapmap now takes a -q command to filter out variants by quality
Modified - MathUtils - cumBinomialProbLog now uses BigDecimal to handle some numerical imprecisions
Modified - PowerBelowFrequency - returns 0.0 if called with a negative number (can't be done from inside the walker itself, but since it's called elsewhere one can't be too careful)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2350 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-14 21:57:20 +00:00
ebanks c7b23d6ca5 Now that VCFGenotypeRecords implement SampleBacked (as they should), a quick fix was needed to get the GenotypeConcordance working when no direct samples were provided in a samples file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2348 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-14 04:27:16 +00:00
ebanks 97618663ef Refactored and generalized the VCF header info code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2346 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-13 21:02:45 +00:00
depristo 05b8782d5f Documentation updates. Moved CountX.java walkers to QC 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2345 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-13 18:40:22 +00:00
kiran 2748eb60e1 Added short documentation for each class so that it appears in the walker command-line documentation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2340 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-12 21:41:07 +00:00
hanna 6955b5bf53 Cleanup of the doc system, and introduce Kiran's concept of a detailed summary 
below the specific command-line arguments for the walker.  Also introduced
@help.summary to override summary descriptions if required.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2337 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-12 04:04:37 +00:00
hanna 0da2105e3c Moving DuplicateQualsWalker to oneoffprojects. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2332 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 19:22:32 +00:00
hanna f97ac939fa Punch up the help documentation for CombineDuplicates. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2325 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 17:09:35 +00:00
aaron 86dc98bfb5 update the documentation for CombineDuplicates for the new help system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2324 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 17:01:42 +00:00
depristo 8f7554d44f A few improvements to pooled concordance calcluations. Now will show you FN with the -V option. BasicGenotype now prints out a reasonable representaiton wiwth toString 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2320 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 23:09:10 +00:00
aaron f64a4c66ac some tweaks for the GATK paper genotyper to better work with shared memory parallelization, added documentation changes for Matt's new help system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2319 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 22:33:51 +00:00
andrewk a7cd172628 Added 8x coverage field and minimum base quality command line option in order to be able to compare to U. Wash. exome metrics. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2318 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 22:14:44 +00:00
ebanks 0fae798b3a 1. Discoverable base calculations don't care about Genotypes (use Variation's PError regardless of whether the call is ref or var - it's the correct value even for ref calls). 
2. Call a base genotypable if any of the Genotypes is above the threshold (you can't assume there's a single Genotype associated with the Variation).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2306 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 04:26:06 +00:00
ebanks 78d5ac9bc2 Don't check het count when there are multiple Genotypes per Variation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2304 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-10 04:07:47 +00:00
ebanks 8d67d9ade3 -Minor fix in UG for all-bases mode 
-Make minConfidenceScore in VariantEval a double so non-integer values can be used (requested by Steve H).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2290 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 03:49:10 +00:00
ebanks e8822a3fb4 Stage 3 of Variation refactoring: 
We are now VCF3.3 compliant.
(Only a few more stages left.  Sigh.)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2287 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-08 21:43:28 +00:00
depristo 8f461d3c40 Critical bug fix for VariantEval dbSNP calculations. Moved the system over to the new improved ROD iterators, resulting in dbSNP rates jumping 5% or so, due to masking of true SNPs by preceding indels. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2274 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-07 03:36:38 +00:00
hanna 8089aa3c50 Adding support to override the help text. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2273 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-07 00:16:26 +00:00
ebanks b6f8e33f4c Stage 2 of Variation refactoring: 
VCFRecord now implements Variation, VCFGenotypeRecord now implements Genotype.

Because of this change, RodVCF is now just a wrapper around the VCFRecord and does nothing else.  Also, one can call toVariation on the VCFGenotypeRecord and it returns the VCFRecord.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2271 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-06 06:48:03 +00:00
hanna 3b440e0dbc Add a taglet to allow users to override the display name in command-line help. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2270 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-06 04:12:10 +00:00
ebanks 08f2214f14 Stage 1 of massive Variation/Genotype refactoring. 
This stage consists only of the code originating in the Genotyper and flowing through to the genotype writers.  I haven't finished refactoring the writers and haven't even touched the readers at all.

The major changes here are that
1. Variations which are BackedByGenotypes are now correctly associated with those Genotypes
2. Genotypes which have an associated Variation can actually be associated with it (and then return it when toVariation() is called).

The only integration tests which need to be updated are MSG-related (because the refactoring now made it easy for me to prevent MSG from emitting tri-allelic sites).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2269 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-06 03:12:41 +00:00
ebanks aef4be5610 Moved CoarseCoverageWalker to core and packaged both coverage walkers in coverage/ 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2249 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 17:53:36 +00:00
ebanks df4e001a07 Renamed to more accurately describe its function. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2248 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 17:34:49 +00:00
ebanks c2017cc91b PrintCoverageWalker functionality moved to DepthOfCoverageWalker. Added integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2247 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 17:23:59 +00:00
ebanks 01cf5cc741 1. Merged CoverageHistogram into DepthOfCoverageWalker 
2. Fixed bug in histogram calculation for small intervals
3. Better output in DoCWalker
4. Comments added to code



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2245 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 17:01:53 +00:00
ebanks 44b9f60735 PercentOfBasesCovered functionality moved to DepthOfCoverageWalker. Added integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2244 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 16:11:09 +00:00
ebanks 126d1eca35 Move to core (qc/) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2243 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 15:45:58 +00:00
ebanks 9da5cc25ad More archiving (with permission from Andrey) plus a move to core. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2242 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 15:40:27 +00:00
ebanks d7e4cd4c82 Moving some useful and stable walkers to core: 
- ClipReads
- PrintRODs (generalized to print all RODs that are Variations)
- FixBAMSortOrderTag (added documentation to walker so that people know what it does and why)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2238 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 03:00:45 +00:00
depristo c776f9fb90 Simple utilities for dealing with Complete Genomics data 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2230 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 22:51:41 +00:00
ebanks a09fee2b5e Moved some more walkers to oneoffprojects and killed an old indel-related walker that isn't being used. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2228 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 20:28:07 +00:00
ebanks a3343c75db Move and rename a hybrid-selection-specific coverage calculation to hybridselection/ 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2225 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 20:11:22 +00:00
ebanks 2c83f2f2bc Move MSG - plus now obsolete classes which it depends on -- to oneoffprojects (with permission from Jared). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2224 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 20:04:22 +00:00
jmaguire c180a76b05 Added option "append": if set, and the specified discovery output already exists, don't re-call anything that's already present in that file. Append new calls to it. 
Great for resuming long jobs that died partway through.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2219 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 18:56:19 +00:00
ebanks 0a2304eff8 - Rename minConfidenceScore in VariantEval to minPhredConfidenceScore 
- Moved validation walkers to new qc dir
- Killed unused test



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2218 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 17:59:19 +00:00
aaron d487428468 remove incorrect parentheses 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2211 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 06:46:32 +00:00
ebanks b979bd2ced - Optimized implementation of -byReadGroup in DoCWalker 
- Added implementation of -bySample in DoCWalker
- Removed CoverageBySample and added a watered down version to the examples directory



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2209 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 03:39:24 +00:00
ebanks ba8a8febc6 Thanks to Steve Hershman for finding this bug: 
getNegLog10PError() does not equal the confidence score (you need to multiply by 10 as confidence is traditionally phred scaled).  Probably we should change the method to be getNeg10Log10PError().  Anyone have strong feelings on this?



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2207 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 01:59:03 +00:00
ebanks 3303808a8f Yet more walkers moved to oneoffprojects. 
Made hybridselection subdir in playground.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2205 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 21:29:12 +00:00
ebanks 05923f7fba Started transition to oneoffprojects. 
Moved/killed a few other walkers (with permission).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2204 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 21:19:02 +00:00
jmaguire 74f6526e09 VCFHomogenizer: A class that extends InputStream and dynamically re-writes pilot1 VCF's to be on-spec. 
VCFTool: A command-line tool with various useful VCF functions (validate, grep, concordance).




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2202 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 17:55:42 +00:00
ebanks e581cceab6 Got Kris's permission to delete these walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2200 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 16:57:28 +00:00
chartl 21a9a717e4 Some minor changes and test: 
- DepthOfCoverage is now by reference (so locus-by-locus output correctly reports zero-coverage bases)
  - VariantsToVCF now lets you bind variants with any string except intervals and dbsnp (not just NA######)
  - A PileupWalker integration test on a particularly nasty FHS site
  - Two second-base annotation related integration tests on that same site
       + outputs were all hand-validated in matlab; within a certain tolerance for the annotations




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2197 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 15:15:54 +00:00
ebanks 084337087e Removing deprecated code and walkers for which I had the green light from repository. 
Moved piecemealannotator and secondarybases to archive.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2195 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 05:58:20 +00:00
ebanks 2c16c18a04 Move Andrey's old indel code (plus MSG accuracy test, which depends on it) to archive. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2194 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 05:29:00 +00:00
depristo af22ca1b47 Bug fixes for VariantEval. dbCoverage now reports dbSNP rate, not some wierd eval_snps_in_db as before. We now separate non-indel and non-snp db sites in dbcoverage. Some dbSNP records don't fit into these two categories. Also fixed a consistency issue where novel / known sites where being determined solely by whether dbSNP had a record there, rather than the stricter dbcoverage screen for isSNP(). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2180 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-30 01:39:01 +00:00
chartl 27651d8dc2 Oops. numReads is now called size 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2175 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-29 06:59:17 +00:00
chartl 21744e024b Quick walker that determines % of bases covered at (user - defined depth)x . I've been maintaining it in my directories alone, but now that i've accidentally deleted it twice, into playground it goes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2174 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-29 06:51:19 +00:00
depristo db40e28e54 ReadBackedPileup in all its glory. Documented, aligned with the output of LocusIteratorByState, and caching common outputs for performance 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2165 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-25 20:54:44 +00:00
aaron cfbd9332b0 small cleanups for the GATK paper genotyper; switched to the managed output system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2156 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-25 08:04:13 +00:00