picard.fastq

Class BamToBfqWriter

java.lang.Object

picard.fastq.BamToBfqWriter

public class BamToBfqWriter
extends java.lang.Object

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. This relies on the unmapped BAM file having all paired reads together in order.

Constructor Summary

Constructors

Constructor and Description
BamToBfqWriter(java.io.File bamFile, java.lang.String outputPrefix, boolean pairedReads, java.lang.String namePrefix, boolean includeNonPfReads) Constructor
BamToBfqWriter(java.io.File bamFile, java.lang.String outputPrefix, java.lang.Integer total, java.lang.Integer chunk, boolean pairedReads, java.lang.String namePrefix, boolean includeNonPfReads, boolean clipAdapters, java.lang.Integer basesToWrite) Constructor

Method Summary

Methods

Modifier and Type	Method and Description
void	writeBfqFiles() Writes the binary fastq file(s) to the output directory

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BamToBfqWriter

public BamToBfqWriter(java.io.File bamFile,
              java.lang.String outputPrefix,
              java.lang.Integer total,
              java.lang.Integer chunk,
              boolean pairedReads,
              java.lang.String namePrefix,
              boolean includeNonPfReads,
              boolean clipAdapters,
              java.lang.Integer basesToWrite)

Constructor

Parameters:

bamFile - the BAM file to read from

outputPrefix - the directory and file prefix for the binary fastq files

total - the total number of records that should be written, drawn evenly from throughout the file (null for all).

chunk - the maximum number of records that should be written to any one file

pairedReads - whether these reads are from a paired-end run

namePrefix - The string to be stripped off the read name before writing to the bfq file. May be null, in which case the name will not be trimmed.

includeNonPfReads - whether to include non pf-reads

clipAdapters - whether to replace adapters as marked with XT:i clipping position attribute

BamToBfqWriter

public BamToBfqWriter(java.io.File bamFile,
              java.lang.String outputPrefix,
              boolean pairedReads,
              java.lang.String namePrefix,
              boolean includeNonPfReads)

Constructor

Parameters:

bamFile - the BAM file to read from

outputPrefix - the directory and file prefix for the binary fastq files

pairedReads - whether these reads are from a paired-end run

namePrefix - the barcode of the run (to be stripped off the read name before writing to the bfq file)

includeNonPfReads - whether to include non pf-reads

Method Detail

writeBfqFiles

public void writeBfqFiles()

Writes the binary fastq file(s) to the output directory