Package htsjdk.samtools

Class SamStreams

java.lang.Object

htsjdk.samtools.SamStreams

public class SamStreams
extends Object

Utilities related to processing of InputStreams encoding SAM data

Constructor Summary

Constructors

Constructor	Description
SamStreams()

Method Summary

Modifier and Type	Method	Description
static boolean	isBAMFile(InputStream stream)
static boolean	isCRAMFile(InputStream stream)
static boolean	isGzippedSAMFile(InputStream stream)	Deprecated. use IOUtil.isGZIPInputStream(InputStream) instead
static boolean	sourceLikeBam(SeekableStream strm)
static boolean	sourceLikeCram(SeekableStream strm)

Methods inherited from class java.lang.Object

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

Constructor Details

SamStreams

public SamStreams()

Method Details

isCRAMFile

public static boolean isCRAMFile(InputStream stream)
                          throws IOException

Throws:

IOException

isBAMFile

public static boolean isBAMFile(InputStream stream)
                         throws IOException

Parameters:

stream - stream.markSupported() must be true

Returns:

true if this looks like a BAM file.

Throws:

IOException

isGzippedSAMFile

@Deprecated
public static boolean isGzippedSAMFile(InputStream stream)

Deprecated.

use IOUtil.isGZIPInputStream(InputStream) instead

Checks whether the file is a gzipped sam file. Returns true if it is and false otherwise.

sourceLikeBam

public static boolean sourceLikeBam(SeekableStream strm)

sourceLikeCram

public static boolean sourceLikeCram(SeekableStream strm)