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
ebanks
depristo
chartl
rpoplin
asivache
kiran
hanna
aaron
andrewk