Package htsjdk.samtools

Class BamFileIoUtils

java.lang.Object

htsjdk.samtools.BamFileIoUtils

public class BamFileIoUtils
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static final String	BAM_FILE_EXTENSION	Deprecated. since June 2019 Use FileExtensions.BAM instead.

Constructor Summary

Constructors

Constructor	Description
BamFileIoUtils()

Method Summary

Modifier and Type	Method	Description
static void	blockCopyBamFile(File inputFile, OutputStream outputStream, boolean skipHeader, boolean skipTerminator)
static void	blockCopyBamFile(Path inputFile, OutputStream outputStream, boolean skipHeader, boolean skipTerminator)	Copy data from a BAM file to an OutputStream by directly copying the gzip blocks.
static void	gatherWithBlockCopying(List<File> bams, File output, boolean createIndex, boolean createMd5)	Assumes that all inputs and outputs are block compressed VCF files and copies them without decompressing and parsing most of the gzip blocks.
static boolean	isBamFile(File file)
static void	reheaderBamFile(SAMFileHeader samFileHeader, File inputFile, File outputFile, boolean createMd5, boolean createIndex)	Support File input types for backward compatibility.
static void	reheaderBamFile(SAMFileHeader samFileHeader, Path inputFile, Path outputFile)
static void	reheaderBamFile(SAMFileHeader samFileHeader, Path inputFile, Path outputFile, boolean createMd5, boolean createIndex)	Copy a BAM file but replacing the header

Methods inherited from class java.lang.Object

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

Field Details

BAM_FILE_EXTENSION

@Deprecated
public static final String BAM_FILE_EXTENSION

Deprecated.

since June 2019 Use FileExtensions.BAM instead.

See Also:

• Constant Field Values

Constructor Details

BamFileIoUtils

public BamFileIoUtils()

Method Details

isBamFile

public static boolean isBamFile(File file)

reheaderBamFile

public static void reheaderBamFile(SAMFileHeader samFileHeader,
 Path inputFile,
 Path outputFile)

reheaderBamFile

public static void reheaderBamFile(SAMFileHeader samFileHeader,
 File inputFile,
 File outputFile,
 boolean createMd5,
 boolean createIndex)

Support File input types for backward compatibility. Use the same method with Path inputs below.

reheaderBamFile

public static void reheaderBamFile(SAMFileHeader samFileHeader,
 Path inputFile,
 Path outputFile,
 boolean createMd5,
 boolean createIndex)

Copy a BAM file but replacing the header

Parameters:

samFileHeader - The header to use in the new file

inputFile - The BAM file to copy, sans header

outputFile - The new BAM file, constructed with the new header and the content from inputFile

createMd5 - Whether or not to create an MD5 file for the new BAM

createIndex - Whether or not to create an index file for the new BAM

blockCopyBamFile

public static void blockCopyBamFile(File inputFile,
 OutputStream outputStream,
 boolean skipHeader,
 boolean skipTerminator)

blockCopyBamFile

public static void blockCopyBamFile(Path inputFile,
 OutputStream outputStream,
 boolean skipHeader,
 boolean skipTerminator)

Copy data from a BAM file to an OutputStream by directly copying the gzip blocks.

Parameters:

inputFile - The BAM file to be copied

outputStream - The stream to write the copied data to

skipHeader - If true, the header of the input file will not be copied to the output stream

skipTerminator - If true, the terminator block of the input file will not be written to the output stream

gatherWithBlockCopying

public static void gatherWithBlockCopying(List<File> bams,
 File output,
 boolean createIndex,
 boolean createMd5)

Assumes that all inputs and outputs are block compressed VCF files and copies them without decompressing and parsing most of the gzip blocks. Will decompress and parse blocks up to the one containing the end of the header in each file (often the first block) and re-compress any data remaining in that block into a new block in the output file. Subsequent blocks (excluding a terminator block if present) are copied directly from input to output.