SamStreams (htsjdk 3.0.4 API)

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)