18b002c99c
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2012-12-03 10:08:56 -05:00
1bdf17ef53
Reworking of how the likelihood calculation is organized in the HaplotypeCaller to facilitate the inclusion of per allele downsampling. We now use the downsampling for both the GL calculations and the annotation calculations.
2012-12-02 11:58:32 -05:00
8020ba14db
Minor cleanup of SAMDataSource as part of my system review
...
-- Changed a few function from public to protected, as they are only used by the package contents, to simplify the SAMDataSource interface
2012-11-30 15:04:41 -05:00
fc7fab5f3b
Fixed ReadBackedPileup downsampling
...
Downsampling in the PerSampleReadBackedPileup was broken, it didn't downsample anything, always returning a copy the original pileup.
2012-11-30 00:42:05 -05:00
97d29f203e
Add walltime changes to LSF
...
- Check whether the specified attribute is available
- Add pipeline test (disabled due to missing attribute)
2012-11-29 15:23:37 -05:00
c76c808268
Reads are required to be sorted
...
- Remove the extended_only case because it's outside intervals
2012-11-28 13:59:58 -05:00
198923b597
Add ActiveRegionReadState handling
2012-11-28 13:59:57 -05:00
f0395b457a
Adding the work-in-progress, experimental RepeatLengthCovariate to the BQSR so Chris can continue the development.
2012-11-28 13:56:32 -05:00
3463774f2a
Merged bug fix from Stable into Unstable
2012-11-28 13:26:52 -05:00
6030605242
Added quick check for creation of bad BAQ values associated with badly encoded base qualities; hopefully this can help us debug the non-reproducible issue seen by many users.
2012-11-28 13:26:31 -05:00
c676853731
Merged bug fix from Stable into Unstable. Updating md5s
...
Conflicts:
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
2012-11-28 12:54:36 -05:00
a1d6461121
Critical bugfix to AFCalcResult affecting UG/HC quality score emission thresholds
...
As reported by Menachem Fromer: a critical bug in AFCalcResult:
Specifically, the implementation:
public boolean isPolymorphic(final Allele allele, final double log10minPNonRef) {
return getLog10PosteriorOfAFGt0ForAllele(allele) >= log10minPNonRef;
}
seems incorrect and should probably be:
getLog10PosteriorOfAFEq0ForAllele(allele) <= log10minPNonRef
The issue here is that the 30 represents a Phred-scaled probability of *error* and it's currently being compared to a log probability of *non-error*.
Instead, we need to require that our probability of error be less than the error threshold.
This bug has only a minor impact on the calls -- hardly any sites change -- which is good. But the inverted logic effects multi-allelic sites significantly. Basically you only hit this logic with multiple alleles, and in that case it'\s including extra alt alleles incorrectly, and throwing out good ones.
Change was to create a new function that properly handles thresholds that are PhredScaled quality scores:
/**
* Same as #isPolymorphic but takes a phred-scaled quality score as input
*/
public boolean isPolymorphicPhredScaledQual(final Allele allele, final double minPNonRefPhredScaledQual) {
if ( minPNonRefPhredScaledQual < 0 ) throw new IllegalArgumentException("phredScaledQual " + minPNonRefPhredScaledQual + " < 0 ");
final double log10Threshold = Math.log10(QualityUtils.qualToProb(minPNonRefPhredScaledQual));
return isPolymorphic(allele, log10Threshold);
}
2012-11-28 12:08:02 -05:00
79bc878e6a
Allow debugging to be set from the command line
2012-11-27 22:37:41 -05:00
b40d3eb8aa
Merged bug fix from Stable into Unstable
2012-11-27 14:41:07 -05:00
01abcc3e0f
Tests didn't like my note to Geraldine in the output logs; apparently it's tested in integration tests
2012-11-27 14:40:49 -05:00
7e4b9c9e6e
Fix failing unit tests for VariantContextUtilsUnitTest
...
-- Previous version was adding multiple samples with the same name to the variant context
2012-11-27 14:26:23 -05:00
9bfe39411e
Equal overlap should match right/later region
2012-11-27 13:03:13 -05:00
d83ad906ef
Add profile range contract
2012-11-27 13:03:13 -05:00
cc550b4145
Add a read and interval on a different contig
2012-11-27 13:03:13 -05:00
9531e58445
Merged bug fix from Stable into Unstable
2012-11-27 11:00:50 -05:00
4543ece088
Fixing parsing of genomelocs that contain colons in the contig names (which is allowed by the spec) as reported on the forum. Added unit test for this case.
2012-11-27 11:00:33 -05:00
a82ec7ad80
Merged bug fix from Stable into Unstable
2012-11-27 10:27:08 -05:00
e199562c25
I have pulled out all of the documentation URLs and put them into the HelpUtils class as static variables; this way, Appistry can change links as needed to point commercial users to their own internal forum without having to muck things up all over our source. Added some TODOs for Geraldine to update links in the GATK docs that still point to the old wiki. Sorry that I am pushing into stable, but that's what Appistry is pulling from for their release next week (and unstable has been failing forever).
2012-11-27 10:26:17 -05:00
97fd5de260
Merging latest CMI updates with UNSTABLE
2012-11-27 09:08:00 -05:00
b1969a66bd
Update docs
2012-11-27 08:24:41 -05:00
cc72aaefeb
Minor efficiency: use >= instead of > in test
2012-11-27 01:11:23 -05:00
405f3c675d
Fix for GSA-649: GenomeLocSortedSet.overlaps is crazy slow. Also improved GenomeLocSortedSet.sizeBeforeLoc.
2012-11-27 01:07:00 -05:00
e27d677c13
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2012-11-26 12:20:32 -05:00
c3b7dd1374
Misc cleanup in the HaplotypeCaller. Cleaning up unused arguments after recent changes to HC-GenotypingEngine
2012-11-26 12:19:11 -05:00
4f7fa3009a
I forget why I thought that the VariantAnnotator couldn't run multi-threaded because it works just fine. Now you can specify -nt with VA.
2012-11-26 11:34:59 -05:00
a3f5932501
Fixed null pointer exception in Integration Tests
...
When running Utils.setupWriter with NO_PG_TAG set, the writer was attempting to create a program record with the null pointer. Fixed.
2012-11-26 11:12:27 -05:00
fedc4fde6c
Merged bug fix from Stable into Unstable
2012-11-25 21:55:55 -05:00
d978cfe835
Soft clipped bases shouldn't be counted in the delocalized BQSR.
2012-11-25 21:55:29 -05:00
9719ba7adc
Remove -number example from the docs since it's no longer supported.
2012-11-22 21:53:42 -05:00
2306518ab6
Fix to deal with 'proper' options of casting
2012-11-22 01:45:18 -05:00
d33a412b5f
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2012-11-22 01:42:29 -05:00
48f271c5bd
Adding 80% support for multi-allelic variants
...
-- Multi-allelic variants are split into their bi-allelic version, trimmed, and we attempt to provide a meaningful genotype for NA12878 here. It's not perfect and needs some discussion on how to handle het/alt variants
-- Adding splitInBiallelic funtion to VariantContextUtils as well as extensive unit tests that also indirectly test reverseTrimAlleles (which worked perfectly FYI)
2012-11-21 17:24:59 -05:00
c68bc95db6
Initial read mapping tests
...
- Failing tests are commented out
2012-11-21 17:16:46 -05:00
3ad9128800
Add some reads
...
- Move intervals and reads to init
- Update intervals and reads
2012-11-21 17:16:46 -05:00
3fa3b00f4a
Add ActiveRegion tests and refactor
2012-11-21 17:16:45 -05:00
e8defcb20d
Test multiple bases and intervals
2012-11-21 17:16:45 -05:00
c08b782743
Count isActive calls directly
2012-11-21 17:16:45 -05:00
4f2229d399
As per the TODO message, I removed a check that was no longer necessary. Now ID is an allowable INFO field key.
2012-11-21 16:01:26 -05:00
06261b58c2
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2012-11-21 15:57:08 -05:00
ed50814ccb
Finally found a case where user errors were being masked behind other errors and could debug. It turns out that the checkForMaskedUserErrors() method needs to run recursively over all levels (calling exception.getCause()) to check for the original cause.
2012-11-21 15:57:05 -05:00
c8be7c3102
Keep SNPs and indels separately for batch merging; Add options to DepthOfCoverage to count fragments (to not double-count overlapping reads of same fragment); DepthOfCoverage should now support ReducedReads; Replace recusrion with loop in DoC/package.scala (for lists longer than 5000 elements)
2012-11-21 15:56:53 -05:00
2e1a055aca
Merged bug fix from Stable into Unstable
2012-11-20 23:20:33 -05:00
c54fc94505
Protect against features that start off the end of the read (otherwise, Arrays.fill fails)
2012-11-20 23:19:59 -05:00
c2efb04657
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2012-11-20 22:43:15 -05:00
72e2d569c5
The user can now set the maximum allowable cycle on the command-line with --maximum_cycle_value. This value is (now) enforced in the Cycle covariate and a User Error is thrown if the maximum value is passed (with a helpful error message). Added unit tests to cover this new functionality.
2012-11-20 22:41:57 -05:00
Ryan Poplin
Mark DePristo
Mauricio Carneiro
Joel Thibault
Eric Banks
Menachem Fromer