- queryContained
query containing - get reads contained by the specified interval
- queryOverlapping
query containing - get reads contained by the specified interval
- <init>
create the fake iterator, given the mapping of chromosomes and read counts
- ensureUntouched
make sure we haven't been used as an iterator yet; this is to miror the
MergingSamIterator2 action.
- hasNext
override the hasNext, to incorportate our limiting factor
- initialize
initialize the query iterator
- initializeUnmapped
initialize the iterator to an unmapped read position
- matches
given a read and the query type, check if it matches our regions
- next
- reset