5b78354efd
Fixed NPE in index check with RefWalkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2384 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 22:37:45 +00:00
e6127cd6c5
Temporary hack for Tim Fennell: introduce a sharding strategy that stuffs all data into a single
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shard for cases when the index file isn't available. Works for the case in question, but is not
guaranteed to work in general. Will be replaced once the new sharding system comes online.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2383 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 21:55:42 +00:00
bef1c50b3b
Some cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2382 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 21:41:06 +00:00
bb92e31118
Optimizations:
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1. push the ReadBackedPileup filtering up into the ReadFilters for read-based filters
2. stop querying the cigar for its length (just do it once)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2381 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 21:39:58 +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
ee47eb4367
Make filters used available to the walker via getToolkit().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2379 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 21:26:04 +00:00
b626fc0684
Joint Estimate is now the default calculation model.
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Reworked all of the integration tests so that they're now more comprehensive, cover more of what we wan to test, and don't take forever to run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2376 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 19:41:02 +00:00
e051311e8c
Added convenience methods in RodVCF to pull out all of the VCF data from the VCFRecord (e.g. getID(), getSamples(), getInfoValues())
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2374 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 17:58:41 +00:00
bb312814a2
UG is now officially in the business of making good SNP calls (as opposed to being hyper-aggressive in its calls and expecting the end-user to filter).
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Bad/suspicious bases/reads (high mismatch rate, low MQ, low BQ, bad mates) are now filtered out by default (and not used for the annotations either), although this can all be turned off.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2373 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 17:28:09 +00:00
af440943a4
Fixing a bug that Steven uncovered; we had an abigous contract for peek() in PushbackIterator, and SeekableRODIterator wasn't checking to see if it's PushbackIterator hasNext() was true before calling peek().
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Changed peek() to element() to be consistant with the Java standards of the Queue and Stack classes (element() throws an exception if a record isn't available).
Also updated some of the ROD iterator next() methods to throw NoSuchElementException if next() is called when a record isn't available.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2372 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 23:04:40 +00:00
1035abc85f
Add minimum base quality thresholding to depth of coverage via getBaseAndMappingFilteredPileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2371 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 22:58:30 +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
9b0bdbbf29
Fix for homopolymer bug: ref was lowercase, alt allele was uppercase, so alt != ref. Yuck.
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This is a temporary fix - pushed more elegant solution over to Matt.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2360 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 19:02:23 +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
b234019cf5
Readded locus printing suppression to DoC walker
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(and removed unused import from UG)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2358 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 14:50:56 +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
bf7bab754e
Made getPileupWithoutMappingQualityZeroReads() and getPileupWithoutDeletions() more efficient, per Mark's cue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2356 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 04:35:21 +00:00
874552ff75
Pull the genotype (and genotype quality) calculation out of the VCF code and into the Genotyper.
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[Also, enable Mark's new UG arguments]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2355 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 04:29:28 +00:00
2cbc85cc7a
min mapping quality and min base quality arguments for UG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2354 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 03:57:27 +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
1389ac6bdf
Hurrr -- this uses power as part of its output. Changes to the power calculation broke the md5s RIGHT AFTER I HAD FIXED THEM arghflrg.
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Will fix again.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2351 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-14 22:42:50 +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
8e44bfd2ef
CycleCovariate and PrimerRoundCovariate now correctly handle negative strand 454 and SOLID reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2349 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-14 21:52:30 +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
bd7b07f3f1
added PrimitivePair.Long and a few shortcut utility methods to PrimitivePairs: add(pair), subtract(pair), assignFrom(pair)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2347 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-14 00:15:44 +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
92307361a4
In preparation for move
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2344 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-13 18:28:06 +00:00
45199136f0
Completed my documentation responsibilities - based on Mark's reasonable assignment and not the one Matt made up while on Meth.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2342 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-13 04:13:30 +00:00
bd2a46ab4c
I want to move over to hpprojects tonight, so I'm checking in various changes all in one go:
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1. Initial code for annotating calls with the base mismatch rate within a reference window (still needs analysis).
2. Move error checking code from rodVCF to VCFRecord.
3. More improvements to SNP Genotype callset concordance.
4. Fixed some comments in Variation/Genotype
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2341 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-13 02:52:18 +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
78e94b5a84
TableRecalibration now puts the full list of walker arguments into the PG tag of the bam file it creates. Thanks Matt and Eric. Also, the default nback for the HomopolymerCovariate is 8, down from 10.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2339 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-12 17:29:41 +00:00
014013630f
Added hieracrchy to the covariate classes: Required, Standard, and Experimental. Required covariates (rg and reported quality) are added for the user whether or not they are specified in the -cov list. There is now a -standard option in CountCovariates which will add in all of the standard covariates so the user doesn't have to type them all out or even know which ones are the standard. There is logger output to say which covariates are being used of course. The list of covariates used is also added to the PG tag in the bam file produced by TableRecalibration.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2338 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-12 16:34:05 +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
cdfe204d19
Incorporated feedback from Kiran. Use the Javadoc first sentence extraction capability to just show the first sentence from each line of Javadoc. @help.description can still be used to produce exceptionally verbose descriptions.
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Also increased the line width as much as I could tolerate (100 characters -> 120 characters).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2336 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 21:59:55 +00:00
4fa4e95fbc
Updated AnalyzeCovariates to extend org.broadinstitute.sting.utils.cmdLine.CommandLineProgram and use the standard argument parsing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2335 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 21:57:18 +00:00
38d9f7b903
Renamed ReferenceContext's getSimpleBase() method to getBaseIndex()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2334 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 20:14:39 +00:00
09811b9f34
Now that we always output the VCF header, make sure that we correctly handle the situation where there are no records in the file. Added unit tests as well.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2333 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 19:51:05 +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
60c3eb4b60
Added help.description to the recalibration walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2331 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 19:02:29 +00:00
2ea7632b76
The SNP genotype concordance module is now more comprehensive.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2330 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 18:34:33 +00:00
590aeee7d2
Documentation for more basic walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2329 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 18:15:40 +00:00
d1815f3559
More documentation for walkers that I'm familiar with in the collection of core walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2328 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 18:02:33 +00:00
956c36a2c8
Help for the qc package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2327 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 17:32:47 +00:00
450ea233a5
Docs for the basic walkers: CountLoci, CountReads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2326 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 17:17:34 +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
420725441a
documentation updates for the new help system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2323 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 16:15:44 +00:00
23d96b1d43
Help system content for the alignment module.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2322 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 16:01:25 +00:00
2de7e1a178
Move VariantAnnotator over to use a StratifiedAlignmentContext split by sample.
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The only major difference is that we are now able to get accurate allele balance ratios.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2321 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 05:28:28 +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
2869270c11
Fixed deletion depth calculation plus mis-spelling in ReadBackedPileup method.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2315 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 21:11:42 +00:00
31b1d60d28
Generalized the StratifiedAlignmentContext code so that it's easy to add new ways to stratify. Then added an MQ0-free stratification so we don't need to be carrying around 2 different alignment contexts (full vs. mq0-free) anymore.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2314 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 19:50:06 +00:00
0c396f04a2
Fix obvious cut/paste error in output stream management code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2313 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 19:23:13 +00:00
11ac7885b0
Pull out StratifiedAlignmentContext code so other walkers can use it.
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This is basically a wrapper class around AlignmentContext which allows you to stratify a context by e.g. reads on forward vs. reverse strands.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2312 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 19:21:16 +00:00
adb2fdbee7
Before, we were only checking that the reference was present if @Requires required that a reference was present. Now we always check that a reference is present, so that we get an intelligent error message.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2311 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 19:15:48 +00:00
5eac510b2f
Refactor the code I gave Eric yesterday to output command line arguments.
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Convert it from a completely wonky solution to a slightly less wonky solution
that will work in more cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2310 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 18:57:54 +00:00
74b8055b6a
Only show extra walker help if the user didn't specify a walker or specified
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an invalid walker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2309 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 16:43:06 +00:00
e6f541fdca
Forgot to update integration test last night
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2308 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 12:57:10 +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
a45adadf1f
VCFGenotypeRecord already defines all the methods needed to be SampleBacked, so let's annotate it as being SampleBacked. This way, when used as a generic Genotype, sample data can be retrieved.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2305 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 04:16:21 +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
ee691b8899
Added a whole bunch of unit tests for VCF reading.
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We could still use more, but this is a good start.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2303 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 03:31:23 +00:00
f7c44ad019
- Read in arguments for the header based on reflection
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- Hook up Variation and Genotype in SSG
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2300 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 21:35:33 +00:00
408f6f3dee
Refactoring of prior commit: better handling of unnamed package within the help system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2297 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 20:12:35 +00:00
1d2151adcf
Better handling of nulls output by
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2296 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 19:34:56 +00:00
40c2d7a4bc
Fix all-bases-mode and genotype-mode in the UG and add integration tests for them.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2295 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 17:41:30 +00:00
4e54b91ce4
UG now outputs the FORMAT header fields when there's genotype data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2294 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 16:31:07 +00:00
12c49ea485
Added DuplicateReadFilter to filter out reads that are marked as duplicates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2293 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 15:42:53 +00:00
fb900b12e1
VariantFiltration now details the filters it has used in the header of the VCF it produces.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2292 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 15:36:15 +00:00
7a76e13459
Better explanation in the exception being thrown.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2291 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 03:59:36 +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
8a1c876104
Weird. I thought I had updated these md5s...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2289 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 03:31:41 +00:00
717eb1de96
- Depth annotation now includes MQ0 reads
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- Removed MQ0 annotation
- Updated RMS MQ annotation to use new pileup
- UG now outputs all of its arguments as key/value pairs in the header (for VCF)
- Cleaned up VCFGenotypeWriterAdapter interface a bit
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2288 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 02:53:00 +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
9e2f831206
A bit of cleanup in preparation for Picard patch.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2286 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-08 16:09:04 +00:00
d3b78338da
Get rid of characters in the docs that aren't universally compatible with
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character sets used throughout the group.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2285 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 21:41:07 +00:00
d75d3a361a
Clean up some of the walker help output based on additional experience and
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feedback received. Also, add a flag to build.xml to disable generation of
docs on demand (use ant -Ddisable.doc=true to disable docs).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2284 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 21:33:11 +00:00
a3e88c0b1c
Cleanup results of bad merge.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2281 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 19:30:49 +00:00
10be5a5de9
Move some files around to reflect our growing help infrastructure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2280 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 19:23:12 +00:00
1d5b9883db
Added --solid_recal_mode argument to experiment with different ways of dealing with solid reference bias. Currently the default option is DO_NOTHING which means use the same behavior as the old recalibrator. Eventually the new methods in RecalDataManager will be moved over to a SolidUtils class. Added transition and transversion methods to BaseUtils that work like simpleComplement, used with the color space in my solid methods. Also, initial check-in of HomopolymerCovariate.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2276 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 14:26:27 +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
c0528cd88e
Updated the CallsetConcordance classes to use new VCF Variation code... and uncovered a whole bunch of VCF bugs in the process. I'm not convinced that I got them all, so I'll unit test like crazy when the refactoring is done.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2272 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-06 11:43:40 +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
b04de77952
First pass at a reorganized walker info display. Groups walkers by package
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and displays walker data extracted from the JavaDoc. Needs a bit of help,
both in content and flexibility of package naming.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2267 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 23:24:29 +00:00
hanna
ebanks
andrewk
aaron
sjia
depristo
chartl
rpoplin
asivache
kiran