Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
The key type. Keys are not written.
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
The key type. Keys are not written.
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
The key type. Keys are not written.
A trait that writes reads using an Htsjdk SAMFileWriter.
A trait that writes reads using an Htsjdk SAMFileWriter.
The recursive type of the class that implements this trait.
Companion object that builds an InFormatter that writes data where the metadata is contained in a SAMFileHeaderWritable.
Companion object that builds an InFormatter that writes data where the metadata is contained in a SAMFileHeaderWritable.
The type of the underlying InFormatter.
An OutFormatter that automatically infers whether the piped input is SAM or BAM.
An OutFormatter that automatically infers whether the piped input is SAM or BAM. Autodetecting streamed CRAM is not currently supported.
A class describing an exception where a read's MD tag was recomputed and did not match the MD tag originally attached to the read.
A class describing an exception where a read's MD tag was recomputed and did not match the MD tag originally attached to the read.
The read whose MD tag was recomputed, with original MD tag.
The recomputed MD tag.
Wrapper that adds instrumentation to the BAM output format.
Wrapper that adds instrumentation to the BAM output format.
The key type. Keys are not written.
Wrapper that adds instrumentation to the SAM output format.
Wrapper that adds instrumentation to the SAM output format.
The key type. Keys are not written.
Wrapper that adds instrumentation to the CRAM output format.
Wrapper that adds instrumentation to the CRAM output format.
The key type. Keys are not written.
Wrapper that adds instrumentation to the CRAM output format.
Wrapper that adds instrumentation to the CRAM output format.
The key type. Keys are not written.
A bin to put quality scores in.
A bin to put quality scores in.
The lowest quality score in the bin.
The highest quality score in the bin.
The score to assign to all these bases.
InFormatter companion for building an InFormatter that streams BAM.
InFormatter companion that creates an InFormatter that writes FASTQ.
Companion object for creating quality score bins.
InFormatter companion for building an InFormatter that streams SAM.
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
The key type. Keys are not written.