Description
positionIsOutsideFrInsert
is actually positionIsInsideFrInsert
fgbio/src/main/scala/com/fulcrumgenomics/bam/pileup/PileupBuilder.scala
Lines 123 to 128 in 3a74fd2
The filter is used in a way that is reversed so that the current tests still work as designed.
fgbio/src/main/scala/com/fulcrumgenomics/bam/pileup/PileupBuilder.scala
Lines 203 to 205 in 3a74fd2
Additionally there is a redundant rec.isFrPair
call (this is done inside the method).
I came across this because I was tracking down some aberrant alleles in a pileup. Should reads mapped to separate chromosomes be rejected by this filter, or should that be a separate filter (likely in quickAcceptRecord
)? Currently these are accepted even if includeMapPositionsOutsideFrInsert
is false
, which i think may be misleading.