Package htsjdk.samtools

Class SamFiles

java.lang.Object

htsjdk.samtools.SamFiles

public class SamFiles
extends Object

Constructor Summary

Constructors

Constructor	Description
SamFiles()

Method Summary

Modifier and Type	Method	Description
static File	findIndex(File samFile)	Finds the index file associated with the provided SAM file.
static Path	findIndex(Path samPath)	Finds the index file associated with the provided SAM file.

Methods inherited from class java.lang.Object

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

Constructor Details

SamFiles

public SamFiles()

Method Details

findIndex

public static File findIndex(File samFile)

Finds the index file associated with the provided SAM file. The index file must exist and be reachable to be found. If the file is a symlink and the index cannot be found, try to unsymlink the file and look for the bai in the actual file path.

Returns:

The index for the provided SAM, or null if one was not found.

findIndex

public static Path findIndex(Path samPath)

Finds the index file associated with the provided SAM file. The index file must exist and be reachable to be found. If the file is a symlink and the index cannot be found, try to unsymlink the file and look for the bai in the actual file path.

Returns:

The index for the provided SAM, or null if one was not found.