…repo Adding sysinternals:junction:1.04:exe to local repo.
With Geraldine's blessing, works around issue where the repo for this exe keeps going down.
Minor documentation clarifications in HC and a typo fix in SelectVariants
Improvements to documentation of variant annotations
…ivity Adding total sensitivity option to ROCCurveNA12878 to help with Mauricio...
…s_fix Improved scatter contigs algorithm to be fairer when splitting many contigs into few parts.
…were run. Fixed off by one error in size calculation IntervalUtils.scatterContigIntervals(). In test for fewer files than intervals, adjusted expected intervals. In test for more files than intervals, adjusted expected exception.
…e number of contigs into a small number of parts. See also: http://gatkforums.broadinstitute.org/discussion/comment/16010 Signed-off-by: Khalid Shakir <email@example.com>
- Added or modified explanations for majority of variant annotations - Generalized NBaseCount to include all tech platforms (not just SOLiD)
Switch GATKDocs publishing to new gsaweb VM
Do not process a variant if it is too large (> readLength), and log an e...
Fix GenotypeGVCF bugs in -allSites mode
Changed license of gsalib R package from BSD to MIT
Added -disableOptimizations argument to HaplotypeCaller.
…now getting output in -allSites mode.
…n error remove final keyword before refMap and altMap, constructHaplotype() changes their values return ArtificialHaplotype from constructHaplotype instaed of passing as an argument Add logic so arraycopy does not throw an IndexOutOfBoundsException, add test for a long insert
- PT 75827540
* 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
…eVariants Throw UserException if input VCFs have duplicate samples but no genotype...
…ypemergeoption is specified
Decrease interval on CGP integration test to reduce test execution time
…cio's analyses. -- We now keep a tally of uncalled sites so that they can be factored into the denominator of the sensitivity/specificity metric
Updated license files and text
In ROCCurveNA12878, if VQSLOD value is not present default to using the ...
…he QUAL field instead to rank the variants.