public class BamFileIoUtils extends Object
Modifier and Type | Field | Description |
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static String |
BAM_FILE_EXTENSION |
Constructor | Description |
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BamFileIoUtils() |
Modifier and Type | Method | Description |
---|---|---|
static void |
blockCopyBamFile(File 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) |
|
static void |
reheaderBamFile(SAMFileHeader samFileHeader,
File inputFile,
File outputFile,
boolean createMd5,
boolean createIndex) |
Copy a BAM file but replacing the header
|
public static final String BAM_FILE_EXTENSION
public static boolean isBamFile(File file)
public static void reheaderBamFile(SAMFileHeader samFileHeader, File inputFile, File outputFile)
public static void reheaderBamFile(SAMFileHeader samFileHeader, File inputFile, File outputFile, boolean createMd5, boolean createIndex)
samFileHeader
- The header to use in the new fileinputFile
- The BAM file to copy, sans headeroutputFile
- The new BAM file, constructed with the new header and the content from inputFilecreateMd5
- Whether or not to create an MD5 file for the new BAMcreateIndex
- Whether or not to create an index file for the new BAMpublic static void blockCopyBamFile(File inputFile, OutputStream outputStream, boolean skipHeader, boolean skipTerminator)
inputFile
- The file to be copiedoutputStream
- The stream to write the copied data toskipHeader
- If true, the header of the input file will not be copied to the output streamskipTerminator
- If true, the terminator block of the input file will not be written to the output streampublic static void gatherWithBlockCopying(List<File> bams, File output, boolean createIndex, boolean createMd5)