All Methods Instance Methods Abstract Methods Default Methods
Modifier and Type	Method	Description
`void`	`close()`
`SAMFileHeader`	`getFileHeader()`
`SAMFileSpan`	`getFilePointerSpanningReads()`
`BAMIndex`	`getIndex()`
`CloseableIterator<SAMRecord>`	`getIterator()`
`CloseableIterator<SAMRecord>`	`getIterator(SAMFileSpan fileSpan)`
`ValidationStringency`	`getValidationStringency()`
`boolean`	`hasIndex()`
`default boolean`	`isQueryable()`
`CloseableIterator<SAMRecord>`	`query(QueryInterval[] intervals, boolean contained)`
`CloseableIterator<SAMRecord>`	`queryAlignmentStart(String sequence, int start)`
`CloseableIterator<SAMRecord>`	`queryUnmapped()`
`SamReader.Type`	`type()`

CloseableIterator<SAMRecord> getIterator()

CloseableIterator<SAMRecord> getIterator(SAMFileSpan fileSpan)

SAMFileSpan getFilePointerSpanningReads()

CloseableIterator<SAMRecord> query(QueryInterval[] intervals,
                                   boolean contained)

CloseableIterator<SAMRecord> queryAlignmentStart(String sequence,
                                                 int start)

CloseableIterator<SAMRecord> queryUnmapped()

ValidationStringency getValidationStringency()

Interface SamReader.PrimitiveSamReader