Package htsjdk.samtools
Class SamFiles
- java.lang.Object
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- htsjdk.samtools.SamFiles
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public class SamFiles extends Object
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Constructor Summary
Constructors Constructor Description SamFiles()
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Method Summary
All Methods Static Methods Concrete Methods 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.
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Method Detail
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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.
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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.
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