- <init>
Prepare to read BAM from a stream (not seekable)
- close
- createIndexIterator
Prepare to iterate through SAMRecords that match the given intervals.
- getFileSpan
Use the index to determine the chunk boundaries for the required intervals.
- findVirtualOffsetOfFirstRecord
Reads through the header and sequence records to find the virtual file offset of
the first record in
- getFileHeader
- getIndex
Retrieves the index for the given file type. Ensure that the index is of the
specified type.
- hasIndex
- readHeader
Reads the header of a BAM file from a stream
- assertIntervalsOptimized
- createStartingAtIndexIterator
Prepare to iterate through SAMRecords in the given reference that start exactly
at the given start c
- enableIndexCaching
If true, uses the caching version of the index reader.