Adding first pass of stub and storage classes for the GenotypeWriters so that UG can be parallelizable. Not hooked up yet, so UG is unchanged.
The mergeInto() code in the storage class is ugly, but it's all Tribble's fault. We can clean it up later if this whole thing works.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2400 348d0f76-0448-11de-a6fe-93d51630548a
2. isNoCall() added to Genotype interface so that we can distinguish between ref and no calls (all we had before was isVariant())
3. Added Hardy-Weinberg annotation; still experimental - not working yet so don't use it.
4. Move 'output type' argument out of the UnifiedArgumentCollection and into the UnifiedGenotyper, in preparation for parallelization.
5. Improved some of the UG integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2398 348d0f76-0448-11de-a6fe-93d51630548a
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
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
[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
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
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
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
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
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
- 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
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
character sets used throughout the group.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2285 348d0f76-0448-11de-a6fe-93d51630548a
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
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
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
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
in GenomeAnalysisTK.jar. Still no support for actually displaying the archived javadoc. Also change the approach
to providing package javadocs: retired the deprecated package.html file in favor of Java1.5-style package-info.java.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2263 348d0f76-0448-11de-a6fe-93d51630548a
-Renamed methods to be more consistent.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2214 348d0f76-0448-11de-a6fe-93d51630548a
Also a minor performance optimization.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2201 348d0f76-0448-11de-a6fe-93d51630548a
Moved piecemealannotator and secondarybases to archive.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2195 348d0f76-0448-11de-a6fe-93d51630548a
Finished converting genotyper and annotator code to new ReadBackedPileup system.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2192 348d0f76-0448-11de-a6fe-93d51630548a
I note that all integration/unit tests pass except for BaseTransitionTableCalculatorJava, which is already broken.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2182 348d0f76-0448-11de-a6fe-93d51630548a
Also, Variations should be INSERTIONs or DELETIONs (and not just INDELs).
Technically, VCF records can be indels now.
More changes coming
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2150 348d0f76-0448-11de-a6fe-93d51630548a
1. Only do calculations in UG for alternate allele with highest sum of quality scores (note that this also constitutes a bug fix for a precision problem we were having).
2. Avoid using Strings in DiploidGenotype when we can (it was taking 1.5% of my compute according to JProfiler)
UG now runs in half the time for JOINT_ESTIMATE model.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2141 348d0f76-0448-11de-a6fe-93d51630548a
[As a courtesy I fixed all instances once I was updating GenotypeLikelihoods]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2136 348d0f76-0448-11de-a6fe-93d51630548a
2. UG: don't print slod if lods are infinite (todo: figure out a good guess instead)
3. UG: if probF=0 for 2 alt alleles are both 0 (because of precision), use log values to discriminate
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2116 348d0f76-0448-11de-a6fe-93d51630548a
2. Retired allele frequency range from UG, which wasn't very useful.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2113 348d0f76-0448-11de-a6fe-93d51630548a
Also a 250% improvement in the getBases() and getQuals() of BasicPileup, which was nearly all of the runtime for the genotyper (using primitives instead of objects when possible).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2097 348d0f76-0448-11de-a6fe-93d51630548a
Updated the integration tests that were failing to due to different ordering of genotyping entries in VCF, I'll check in the VCF diff tool I wrote when I get a cycle or two.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2092 348d0f76-0448-11de-a6fe-93d51630548a
2. Allele frequency spectrum is not emitted for single samples (since it doesn't make sense).
3. If in pooled mode, throw an exception of pool size isn't set appropriately.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2072 348d0f76-0448-11de-a6fe-93d51630548a
VariantAnnotator can be called as a standalone walker or by another walker, as it is by the UnifiedGenotyper. UG now no longer computes any of this meta data - it relegates the task completely to the annotator (assuming the output format accepts it).
This is a fairly all-encompassing check in. It involves changes to all of the UG code, bug fixes to much of the VCF code as things popped up, and other changes throughout. All integration tests pass and I've tediously confirmed that the annotation values are correct, but this framework could use some more rigorous testing.
Stage 2 of the process will happen later this week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2053 348d0f76-0448-11de-a6fe-93d51630548a
2. Don't print verbose output from SLOD calculation (it's just a repeat of previous output).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2032 348d0f76-0448-11de-a6fe-93d51630548a
1. Add dbsnp RS ID to VCF output from genotyper; to do this I needed to fix the dbsnp rod which did not correctly return this value.
2. Remove AlleleBalanceBacked and instead generalize the arbitrary info fields backing VCFs (and potentially others) in preparation for refactoring VariantFiltration next week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2028 348d0f76-0448-11de-a6fe-93d51630548a
1. Don't cap q-scores at 99
2. Scale SLOD to allow more resolution in the output
3. UG outputs weighted allele balance (AB) and on-off genotype (OO) info fields for het genotype calls (works for joint estimation model and SSG)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2011 348d0f76-0448-11de-a6fe-93d51630548a
-Don't restrict info fields to 2-letter keys
[about to move these to core]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2002 348d0f76-0448-11de-a6fe-93d51630548a
-Improvement to snp genotype concordance test
And with that, it looks like I get revision #2000.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2000 348d0f76-0448-11de-a6fe-93d51630548a
Now, all output is generalized and all of the intelligence lies where it is supposed to.
Next stage is syncing up old and new models and making sure we're outputting exactly what we should.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1960 348d0f76-0448-11de-a6fe-93d51630548a
A couple of notes:
-Commented out BaseTransitionTableCalculator.scala because it's won't build; Chris could you fix this one (or kill it if it's not needed).
-Removed the PrintReadsScala walker; moved the code over to a ScalaCountLoci walker (which is what the code was really doing).
-Added configurations items to the ivy xml file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1956 348d0f76-0448-11de-a6fe-93d51630548a
-Make rods return the appropriate type of Genotype calls from getGenotype().
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1954 348d0f76-0448-11de-a6fe-93d51630548a
hanna
aaron
ebanks
rpoplin
depristo
chartl
asivache
jmaguire
mmelgar