- <init>
copy constructor
- makeSAMOrBAMWriter
Create either a SAM or a BAM writer based on examination of the outputPath
extension.
- makeBAMWriter
Create a BAMFileWriter that is ready to receive SAMRecords.
- setCreateIndex
Convenience method allowing newSAMFileWriterFactory().setCreateIndex(true);
Equivalent to SAMFileWri
- makeSAMWriter
Create a SAMTextWriter that is ready to receive SAMRecords.
- makeWriter
Create a SAM, BAM or CRAM writer based on examination of the outputPath
extension.
- makeCRAMWriter
Create a CRAMFileWriter on an output file. Note: does not honor factory setting
for USE_ASYNC_IO.
- setCreateMd5File
Sets whether to create md5Files for BAMs from this factory.
- setUseAsyncIo
Turn on or off the use of asynchronous IO for writing output SAM and BAM files.
If true then each SA
- initWriter
Initialize SAMTextWriter or a BAMFileWriter and possibly wrap in
AsyncSAMFileWriter
- initializeBAMWriter
- setCompressionLevel
set compression level 0!none 9: max