public class BAMIndexer
extends java.lang.Object
| Constructor and Description |
|---|
BAMIndexer(java.io.File output,
SAMFileHeader fileHeader) |
BAMIndexer(java.io.OutputStream output,
SAMFileHeader fileHeader)
Prepare to index a BAM.
|
BAMIndexer(java.nio.file.Path output,
SAMFileHeader fileHeader) |
| Modifier and Type | Method and Description |
|---|---|
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.
|
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.
|
void |
processAlignment(SAMRecord rec)
Record any index information for a given BAM record.
|
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