public class BAMIndexer
extends java.lang.Object
Constructor and Description |
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BAMIndexer(java.io.File output,
SAMFileHeader fileHeader) |
BAMIndexer(java.io.OutputStream output,
SAMFileHeader fileHeader)
Prepare to index a BAM.
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BAMIndexer(java.nio.file.Path output,
SAMFileHeader fileHeader) |
Modifier and Type | Method and Description |
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static void |
createAndWriteIndex(java.io.File input,
java.io.File output,
boolean textOutput)
Generates a BAM index file, either textual or binary, from an input BAI file.
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static void |
createIndex(SamReader reader,
java.io.File output)
Generates a BAM index file from an input BAM file
|
static void |
createIndex(SamReader reader,
java.io.File output,
Log log)
Generates a BAM index file from an input BAM file
|
static void |
createIndex(SamReader reader,
java.nio.file.Path output)
Generates a BAM index file from an input BAM file
|
static void |
createIndex(SamReader reader,
java.nio.file.Path output,
Log log)
Generates a BAM index file from an input BAM file
|
void |
finish()
After all the alignment records have been processed, finish is called.
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void |
processAlignment(SAMRecord rec)
Record any index information for a given BAM record.
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public BAMIndexer(java.nio.file.Path output, SAMFileHeader fileHeader)
output
- binary BAM Index (.bai) filefileHeader
- header for the corresponding bam filepublic BAMIndexer(java.io.File output, SAMFileHeader fileHeader)
output
- binary BAM Index (.bai) filefileHeader
- header for the corresponding bam filepublic BAMIndexer(java.io.OutputStream output, SAMFileHeader fileHeader)
output
- Index will be written here. output will be closed when finish() method is called.fileHeader
- header for the corresponding bam file.public void processAlignment(SAMRecord rec)
rec
- The BAM recordpublic void finish()
public static void createAndWriteIndex(java.io.File input, java.io.File output, boolean textOutput)
output
- BAM Index (.bai) file (or bai.txt file when text)textOutput
- Whether to create text output or binarypublic static void createIndex(SamReader reader, java.nio.file.Path output)
reader
- SamReader for input BAM fileoutput
- Path for output index filepublic static void createIndex(SamReader reader, java.io.File output)
reader
- SamReader for input BAM fileoutput
- File for output index filepublic static void createIndex(SamReader reader, java.nio.file.Path output, Log log)
reader
- SamReader for input BAM fileoutput
- Path for output index file