Package htsjdk.samtools

Class SamReader.ReaderImplementation

java.lang.Object

htsjdk.samtools.SamReader.ReaderImplementation

All Implemented Interfaces:

SamReader.PrimitiveSamReader

Direct Known Subclasses:

BAMFileReader, CRAMFileReader, HtsgetBAMFileReader, SRAFileReader

Enclosing interface:

SamReader

public abstract static class SamReader.ReaderImplementation
extends Object
implements SamReader.PrimitiveSamReader

Internal interface for SAM/BAM/CRAM file reader implementations, as distinct from non-file-based readers. Implemented as an abstract class to enforce better access control. TODO -- Many of these methods only apply for a subset of implementations, TODO -- and either no-op or throw an exception for the others. TODO -- We should consider refactoring things to avoid this; TODO -- perhaps we can get away with not having this class at all.

Constructor Summary

Constructors

Constructor	Description
ReaderImplementation()

Method Summary

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.samtools.SamReader.PrimitiveSamReader

close, getFileHeader, getFilePointerSpanningReads, getIndex, getIterator, getIterator, getValidationStringency, hasIndex, isQueryable, query, queryAlignmentStart, queryUnmapped, type

Constructor Details

ReaderImplementation

public ReaderImplementation()