Package | Description |
---|---|
htsjdk.samtools |
Modifier and Type | Class and Description |
---|---|
class |
CRAMFileWriter |
class |
SAMFileWriterImpl
Base class for implementing SAM writer with any underlying format.
|
class |
SAMTextWriter
Writer for text-format SAM files.
|
Modifier and Type | Method and Description |
---|---|
SAMFileWriter |
SAMFileWriterFactory.makeBAMWriter(SAMFileHeader header,
boolean presorted,
java.io.File outputFile)
Create a BAMFileWriter that is ready to receive SAMRecords.
|
SAMFileWriter |
SAMFileWriterFactory.makeBAMWriter(SAMFileHeader header,
boolean presorted,
java.io.File outputFile,
int compressionLevel)
Create a BAMFileWriter that is ready to receive SAMRecords.
|
SAMFileWriter |
SAMFileWriterFactory.makeBAMWriter(SAMFileHeader header,
boolean presorted,
java.io.OutputStream stream)
Create a BAMFileWriter for writing to a stream that is ready to receive SAMRecords.
|
SAMFileWriter |
SAMFileWriterFactory.makeSAMOrBAMWriter(SAMFileHeader header,
boolean presorted,
java.io.File outputFile)
Create either a SAM or a BAM writer based on examination of the outputFile extension.
|
SAMFileWriter |
SAMFileWriterFactory.makeSAMWriter(SAMFileHeader header,
boolean presorted,
java.io.File outputFile)
Create a SAMTextWriter that is ready to receive SAMRecords.
|
SAMFileWriter |
SAMFileWriterFactory.makeSAMWriter(SAMFileHeader header,
boolean presorted,
java.io.OutputStream stream)
Create a SAMTextWriter for writing to a stream that is ready to receive SAMRecords.
|
SAMFileWriter |
SAMFileWriterFactory.makeWriter(SAMFileHeader header,
boolean presorted,
java.io.File outputFile,
java.io.File referenceFasta)
Create a SAM, BAM or CRAM writer based on examination of the outputFile extension.
|