PairFormatter

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

gngs.pair.PairFormatter

```
@groovy.transform.CompileStatic
@groovy.util.logging.Log
class PairFormatter
extends RegulatingActor<Paired>
```
Converts reads to FASTQ format, and sends them in batches to a writer.
A buffer is accumulated by appending each read requested to it in FASTQ format, until the buffer exceeds a specified size. In general, this buffer size should be optimised to ensure that the downstream I/O operations are efficient, which generally means writing at least 10KB chunks at least, but up to 1MB may be appropriate depending on the file system and OS.
Authors:
Simon Sadedin

Properties Summary

Properties
Type	Name and description
`boolean`	`addPosition` If true, the original position of the read will be appended to the read name.
`java.lang.StringBuilder`	`buffer`
`java.lang.StringBuilder`	`buffer2`
`int`	`buffered`
`java.lang.String`	`debugRead`
`int`	`formatted`
`int`	`maxBufferSize`
`PairWriter`	`writer`
`PairWriter`	`writer2`

Constructor Summary

Constructors
Constructor and description
`PairFormatter (int bufferSize, PairWriter writer, PairWriter writer2)`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`void`	`flushBuffer()`
	`void`	`flushBufferAndWriter(java.lang.StringBuilder buffer, PairWriter writer)`
	`void`	`onEnd()`
	`final void`	`process(Paired paired)`

- Property Detail
  - boolean addPosition
    
    If true, the original position of the read will be appended to the read name. This allows backtracking of reads to compare between alignments, etc.
  - java.lang.StringBuilder buffer
  - java.lang.StringBuilder buffer2
  - int buffered
  - java.lang.String debugRead
  - int formatted
  - int maxBufferSize
  - PairWriter writer
  - PairWriter writer2
- Constructor Detail
  - PairFormatter(int bufferSize, PairWriter writer, PairWriter writer2)
- Method Detail
  - void flushBuffer()
  - void flushBufferAndWriter(java.lang.StringBuilder buffer, PairWriter writer)
  - @java.lang.Override void onEnd()
  - @groovy.transform.CompileStatic final void process(Paired paired)

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation