* This argument is intended to be used in conjunction with -bamout, and disable early-exit optimizations to allow reference regions to be contained in the output bam
* Also forcibly includes the reference haplotype in the set of haplotypes given to the BAMWriter
* Made -dontTrimActiveRegions visible, as it is likely also desirable in this use case
* Addresses PT 77731660
remove TODO comment after activeProbThreshold
recover static ACTIVE_PROB_THRESHOLD for unit tests
Add min/max values for active_probability_threshold parameter
Move activeProbThreshold parameter to GATKArguemtnCollection
define ACTIVE_PROB_THRESHOLD in unit tests
add construction of argCollection in in ctor
Move arguments from GATKArgumentCollection to ActiveRegionWalker
Throw exception if threshold < 0 or > 1 in ActivityProfile ctor
max propogation distance parameter to ActiveRegionWalker for AcrtivityProfile
Use polymorphic getMaxProbPropagationDistance() so BandPassActivityProfile computes the crrect region size cutoff
Get the maxProbPropagationDistance from the super class's method, instead of directly, this is safer
Removed extraneous command line imports and make maxProbPropagationDistance a hidden argument
remove limit check for activeProbThreshold, not necessary because the check is made when imput as a command line arg
Remove extra 'region' in the doxygen param description for maxProbPropagationDistance
Rename parameters using camel case and add to integration test
Correct documentation for maxReadsInRegionPerSample and minReadsPerAlignmentStart
Change the argument--minReadsPerAlignmentStart in the integration test from 50 to 5
'each genomic location' only pertains to minReadsPerAlignmentStart, not maxReadsInRegionPerSample
The QUAL value calculated by this Exact AF Calculator is very underestimated when
there are more than one alternative allele (non-biallelic sites). The reason is
that the QUAL was roughly calculated by adding the QUALs resulting of each alternative
alleles vs all other alleles, reference and alts, collapsed. This is ok for MLEAC
calculations but not for QUAL.
Now, for calculating the QUAL we collapse all the alternatives as only one. This change
improves sensitivy with a cost of additional false positives, but this is naturally expected.
The resulting QUAL column is much closer to the one returned by the reference implementation.
Story:
https://www.pivotaltracker.com/story/show/75926368.
Changes:
Changed the QUAL calculation as described above.
Updated MD5s.
Fixed MD5s
The problem whas that the MLE table calculation aborted "unlikely"
genotype combinations to aggresively.
This also uncovered another bug where GeneralPloidyExactAFCalculation
makes a slightly different use of StateTracker
as compared to DiploidExactAFCalculation. We have changed StateTracker
generalizing it to be able to work with both using code behaviors.
Story:
-----
* https://www.pivotaltracker.com/story/show/78920568
Changes:
-------
* Fixes in GeneralPloidyExactAFCalculator.
* Needed changes in StateTracker API and its consequences in DiploidExactAFCalculation.
* Updated affected integrated tests' MD5s after fixing the GeneralPloidyExactAF.
* This argument forces GATK to always write every record in the VCF format field, even if some records at the end are missing and could be removed
* Revved htsjdk and picard
* PT 70993484
Changes:
-------
* Updated current unit and integration test to use the new API components.
* Added unit tests for new classes AFPriorProvider and AFCalculatorProviders.
* Added integration test for mixed ploidy GenotypeGVCFs and CombineGVCFs
Changes:
-------
* GenotypingEngine uses now a AFCalc provider instead of
its own thread-local with one-time initialized and fixed
AF calculator.
* All walkers that use a GenotypingEngine now are passing
the appropiate AF calculator provider. For now most
just use a fix calculator (FixedAFCalculatorProvider)
except GenotypeGVCFs as this one now can cope with
mixture of ploidies failing-over to a general-ploidy
calculator when the preferred implementation is not
capable to handle a site's analysis.
to the total-ploidy (added ploidy accross samples).
Changes:
--------
* Instead of calculate a fixed log10 prior array with a fix
total likelihood we use a new component, the AFPriorProvider
to generate the priors for different total plodies on
demand; these are cached however so there is no unecessary
recompute involved.
with mixed ploidies and max-alt-allele number changes dynamically.
Changes:
--------
* Moved the AFCalcFactory.Calculation enum in a top level class
AFCalculatorImplementation.
* Given more reponsabilities to the enum like resolving the constructor
method once per implementation and the best-model selection algorithm.
* Removed test-code only fields and methods from AFCalc; just used to perform
unit-testing and not any actual functionality of this component.
* Removed the fixed ploidy constraint of GeneralPloidyExactAFCalc
implementation... now can deal with mixed ploidies that may change
per site and sample.
* Removed the fixed maxAltAllele restriction by allowing resizing of
the stateTracker structures.
* Due to previous two points now call the the AFCalc object are passed
the default-ploidy to assume in case some genotype in the input
VC does not have it and the max-alt-allele.
* Also due to those changes, removed the now totally useless 3 int
parameters from all AFCalc constructors.
* Cleaned the code a bit from no further used components and methods.
Dangling head merging (like with tails) in now enabled by default.
The --recoverDanglingHeads argument is now deprecated so that users know not to use it anymore.
We now also allow the user to set the minimum branch length for merging. This will be different
for exomes and RNA (see below).
The other changes in the code itself:
1. We no longer allow an arbitrarily large number of mismatches in the dangling head for merging
2. The max number of mismatches allowed in a dangling head is proportional to the kmer size
There will be a difference in the RNA calling pipeline. Instead of invoking '--recoverDanglingHeads'
the user will instead want to use '--minDanglingBranchLength 0'.
Below are the knowledgebase results of the master branch vs. this one.
For NA12878 DNA Exome:
master SNPS TRUE_POSITIVE 36722
master SNPS CALLED_NOT_IN_DB_AT_ALL 2699
master SNPS REASONABLE_FILTERS_WOULD_FILTER_FP_SITE 292
master SNPS FALSE_POSITIVE_SITE_IS_FP 70
branch SNPS TRUE_POSITIVE 36867
branch SNPS CALLED_NOT_IN_DB_AT_ALL 2952
branch SNPS REASONABLE_FILTERS_WOULD_FILTER_FP_SITE 387
branch SNPS FALSE_POSITIVE_SITE_IS_FP 94
As I discussed with Ryan in person, there are a good number of FPs that are called in the new
code, but they nearly all have bad strand bias and should be easily filtered by VQSR.
Note that there is no change for indels.
For NA12878 RNA from Ami:
master SNPS TRUE_POSITIVE 11055
master SNPS CALLED_NOT_IN_DB_AT_ALL 831
master SNPS REASONABLE_FILTERS_WOULD_FILTER_FP_SITE 44
master SNPS FALSE_POSITIVE_SITE_IS_FP 96
branch SNPS TRUE_POSITIVE 11113
branch SNPS CALLED_NOT_IN_DB_AT_ALL 874
branch SNPS REASONABLE_FILTERS_WOULD_FILTER_FP_SITE 47
branch SNPS FALSE_POSITIVE_SITE_IS_FP 92
Again, there's basically no change for indels.
* Arguments involved are --no_cmdline_in_header, --sites_only, and --bcf for VCF files and --bam_compression, --simplifyBAM, --disable_bam_indexing, and --generate_md5 for BAM files
* PT 52740563
* Removed ReadUtils.createSAMFileWriterWithCompression(), replaced with ReadUtils.createSAMFileWriter(), which applies all appropriate engine-level arguments
* Replaced hard-coded field names in ArgumentDefinitionField (Queue extension generator) with a Reflections-based lookup that will fail noisily during extension generation if there's an error
rpoplin
Phillip Dexheimer
ldgauthier
Geraldine Van der Auwera
jmthibault79
Ron Levine
Valentin Ruano-Rubio
Ron Levine
Eric Banks
droazen