public class BamFileIoUtils
extends java.lang.Object
Modifier and Type | Field and Description |
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static java.lang.String |
BAM_FILE_EXTENSION |
Constructor and Description |
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BamFileIoUtils() |
Modifier and Type | Method and Description |
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static void |
blockCopyBamFile(java.io.File inputFile,
java.io.OutputStream outputStream,
boolean skipHeader,
boolean skipTerminator)
Copy data from a BAM file to an OutputStream by directly copying the gzip blocks
|
static void |
gatherWithBlockCopying(java.util.List<java.io.File> bams,
java.io.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.
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static boolean |
isBamFile(java.io.File file) |
static void |
reheaderBamFile(SAMFileHeader samFileHeader,
java.io.File inputFile,
java.io.File outputFile) |
static void |
reheaderBamFile(SAMFileHeader samFileHeader,
java.io.File inputFile,
java.io.File outputFile,
boolean createMd5,
boolean createIndex)
Copy a BAM file but replacing the header
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public static final java.lang.String BAM_FILE_EXTENSION
public static boolean isBamFile(java.io.File file)
public static void reheaderBamFile(SAMFileHeader samFileHeader, java.io.File inputFile, java.io.File outputFile)
public static void reheaderBamFile(SAMFileHeader samFileHeader, java.io.File inputFile, java.io.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(java.io.File inputFile, java.io.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(java.util.List<java.io.File> bams, java.io.File output, boolean createIndex, boolean createMd5)