fcc80e8632
Completely rewritten duplicate traversal, more free of bugs, with integration tests for count duplicates walker validated on a TCGA hybrid capture lane.
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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
57516582c2
Converter from HapMap chip genotype data to VCF added; HapMapGenotypeROD adjusted to not convert from Hg18 to b36 formatting of contigs
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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
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).
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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
4ee6a478e3
Creates a table of reference allele percentage and alternate allele percentage at Hapmap-chip sites in a BAM file.
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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
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.
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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
ee8bcdc61d
PooledConcordance calculations have been reformatted and bugs fixed. Now properly handles monomorphic sites. Also works with -G option now, correctly
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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
9bf2d12c64
Misc. improvements to the LMW code. Support for emitting all sites, regardless of genotype. Min and max quality scores.
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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
c39675d2c1
VCFTool.java got left off of the last commit
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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
4ea31fd949
Pushed header initialization out of the GenotypeWriter constructors and into a writeHeader method, in preparation for parallelization.
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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
98839193b7
compatibility with VCF lib's switch to GenomeLoc.
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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
8787dd4c5e
Various and sundry additions to VCF tools. Some useful to the general public, some one-offs.
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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
36875fca89
Update documentation in the new help system
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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
2deae95df9
Updated documentation
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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
555976d575
One more walker with formatting to fix.
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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
cf46472419
Fix up Sherman's new docs in compliance with javadoc specs.
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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
df79ed8db1
Updated documentation
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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
a80a5f1036
Updated documentation
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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
18f61d2586
Updated documentation
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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
5974c42468
Updated documentation
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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
d8cfd707bc
Updated documentation
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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
4322beeb35
Updated documentation
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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
4148991d81
Now also encodes amino acids, includes documentation.
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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
a810586418
Check-in without javadoc = smackdown
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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
0d2a761460
Bugfix for minBaseQuality to ignore deletion reads. LocusMismatch walker now allows us to skip every nths eligable site
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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
faa638532a
Correct location
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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
1da97ebb85
Walker for calculating non-independent base errors, v1. Will be moved to somewhere not in core
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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
b42fc905e8
Added - new tests (Hapmap was re-added)
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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
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.
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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
97618663ef
Refactored and generalized the VCF header info code.
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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
05b8782d5f
Documentation updates. Moved CountX.java walkers to QC
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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
2748eb60e1
Added short documentation for each class so that it appears in the walker command-line documentation.
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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
6955b5bf53
Cleanup of the doc system, and introduce Kiran's concept of a detailed summary
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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
0da2105e3c
Moving DuplicateQualsWalker to oneoffprojects.
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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
f97ac939fa
Punch up the help documentation for CombineDuplicates.
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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
86dc98bfb5
update the documentation for CombineDuplicates for the new help system.
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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
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
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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
f64a4c66ac
some tweaks for the GATK paper genotyper to better work with shared memory parallelization, added documentation changes for Matt's new help system.
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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
a7cd172628
Added 8x coverage field and minimum base quality command line option in order to be able to compare to U. Wash. exome metrics.
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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
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).
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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
78d5ac9bc2
Don't check het count when there are multiple Genotypes per Variation.
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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
8d67d9ade3
-Minor fix in UG for all-bases mode
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-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
e8822a3fb4
Stage 3 of Variation refactoring:
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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
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.
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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
8089aa3c50
Adding support to override the help text.
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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
b6f8e33f4c
Stage 2 of Variation refactoring:
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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
3b440e0dbc
Add a taglet to allow users to override the display name in command-line help.
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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
08f2214f14
Stage 1 of massive Variation/Genotype refactoring.
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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
aef4be5610
Moved CoarseCoverageWalker to core and packaged both coverage walkers in coverage/
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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
df4e001a07
Renamed to more accurately describe its function.
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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
c2017cc91b
PrintCoverageWalker functionality moved to DepthOfCoverageWalker. Added integration tests.
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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
depristo
andrewk
kiran
ebanks
aaron
jmaguire
sjia
hanna
chartl