public class BamToBfqWriter extends Object
| Constructor and Description |
|---|
BamToBfqWriter(File bamFile,
String outputPrefix,
boolean pairedReads,
String namePrefix,
boolean includeNonPfReads)
Constructor
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BamToBfqWriter(File bamFile,
String outputPrefix,
Integer total,
Integer chunk,
boolean pairedReads,
String namePrefix,
boolean includeNonPfReads,
boolean clipAdapters,
Integer basesToWrite)
Constructor
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| Modifier and Type | Method and Description |
|---|---|
void |
writeBfqFiles()
Writes the binary fastq file(s) to the output directory
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public BamToBfqWriter(File bamFile, String outputPrefix, Integer total, Integer chunk, boolean pairedReads, String namePrefix, boolean includeNonPfReads, boolean clipAdapters, Integer basesToWrite)
bamFile - the BAM file to read fromoutputPrefix - the directory and file prefix for the binary fastq filestotal - 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 filepairedReads - whether these reads are from a paired-end runnamePrefix - 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-readsclipAdapters - whether to replace adapters as marked with XT:i clipping position attributepublic BamToBfqWriter(File bamFile, String outputPrefix, boolean pairedReads, String namePrefix, boolean includeNonPfReads)
bamFile - the BAM file to read fromoutputPrefix - the directory and file prefix for the binary fastq filespairedReads - whether these reads are from a paired-end runnamePrefix - 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