- getFileHeader
- iterator
Iterate through file in order. For a SAMFileReader constructed from an
InputStream, and for any SAM
- close
- hasIndex
- indexing
Exposes the SamReader.Indexing facet of this SamReader.
- query
Iterate over records that match one of the given intervals. This may be more
efficient than querying
- queryOverlapping
Iterate over records that overlap any of the given intervals. This may be more
efficient than queryi
- queryUnmapped
- type
- spliterator
- queryAlignmentStart
Iterate over records that map to the given sequence and start at the given
position. Only valid to c
- queryContained
Iterate over records that are contained in the given interval. This may be more
efficient than query