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.
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
* 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
droazen
Khalid Shakir
Geraldine Van der Auwera
rpoplin
kshakir
Chris Smowton
Sheila Chandran
Laura Gauthier
Ron Levine
Phillip Dexheimer
jmthibault79
Ron Levine
Valentin Ruano-Rubio
Ron Levine