Package htsjdk.samtools

Class SamReader.Type

java.lang.Object

htsjdk.samtools.SamReader.Type

Enclosing interface:

SamReader

public abstract static class SamReader.Type
extends Object

Describes a type of SAM file.

Field Summary

Fields

Modifier and Type	Field	Description
static final SamReader.Type	BAM_CSI_TYPE
static final SamReader.Type	BAM_HTSGET_TYPE
static final SamReader.Type	BAM_TYPE
static final SamReader.Type	CRAM_TYPE
static final SamReader.Type	SAM_TYPE
static final SamReader.Type	SRA_TYPE

Constructor Summary

Constructors

Constructor	Description
Type()

Method Summary

Modifier and Type	Method	Description
abstract String	fileExtension()	The recommended file extension for SAMs of this type, without a period.
boolean	hasValidFileExtension(String fileName)
abstract String	indexExtension()	The recommended file extension for SAM indexes of this type, without a period, or null if this type is not associated with indexes.
abstract String	name()	A string representation of this type.

Methods inherited from class java.lang.Object

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

Field Details

SRA_TYPE

public static final SamReader.Type SRA_TYPE

CRAM_TYPE

public static final SamReader.Type CRAM_TYPE

BAM_TYPE

public static final SamReader.Type BAM_TYPE

SAM_TYPE

public static final SamReader.Type SAM_TYPE

BAM_CSI_TYPE

public static final SamReader.Type BAM_CSI_TYPE

BAM_HTSGET_TYPE

public static final SamReader.Type BAM_HTSGET_TYPE

Constructor Details

Type

public Type()

Method Details

name

public abstract String name()

A string representation of this type.

fileExtension

public abstract String fileExtension()

The recommended file extension for SAMs of this type, without a period.

indexExtension

public abstract String indexExtension()

The recommended file extension for SAM indexes of this type, without a period, or null if this type is not associated with indexes.

hasValidFileExtension

public boolean hasValidFileExtension(String fileName)