| Interface | Description |
|---|---|
| ReadNameEncoder |
| Class | Description |
|---|---|
| BamToBfq |
CommandLineProgram to generate to bfq files for use by the Maq aligner
|
| BamToBfqWriter |
Class to take unmapped reads in BAM file format and create Maq binary fastq format file(s) --
one or two of them, depending on whether it's a paired-end read.
|
| Casava18ReadNameEncoder |
A read name encoder conforming to the standard described by Illumina Casava 1.8.
|
| IlluminaReadNameEncoder |
A read name encoder following the encoding initially produced by picard fastq writers.
|