class Tab5InFormatter extends InFormatter[Fragment, Fragment, FragmentDataset, Tab5InFormatter] with Logging
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def
write(os: OutputStream, iter: Iterator[Fragment]): Unit
Writes alignments to an output stream in Bowtie tab5 format.
Writes alignments to an output stream in Bowtie tab5 format.
In Bowtie tab5 format, each alignment or pair is on a single line. An unpaired alignment line is [name]\t[seq]\t[qual]\n. A paired-end read line is [name]\t[seq1]\t[qual1]\t[seq2]\t[qual2]\n.
The read name for a paired-end read line is the name of the first read with the suffix trimmed.
- os
An OutputStream connected to a process we are piping to.
- iter
An iterator of records to write.
- Definition Classes
- Tab5InFormatter → InFormatter