- createSAMFileWriter
As
#createSAMFileWriter(String,org.broadinstitute.gatk.engine.GenomeAnalysisEngine),
but also sets t
- <init>
Create a new stub given the requested SAM file and compression level.
- getCompressionLevel
Retrieves the desired compression level for
- getFileHeader
Retrieves the header to use when creating the new SAM file.
- getGenerateMD5
Gets whether to generate an md5 on-the-fly for this BAM.
- getIndexOnTheFly
Gets whether to index this output stream on-the-fly.
- getMaxRecordsInRam
Get the maximum number of reads to hold in RAM when sorting a BAM on-the-fly.
- getOutputFile
Retrieves the SAM file to (ultimately) be created.
- getReferenceFile
- initializeReadTransformers
- isPresorted
Whether the BAM file to create is actually presorted.
- processArguments