public class BamToBfqWriter
extends java.lang.Object
Constructor and Description |
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BamToBfqWriter(java.io.File bamFile,
java.lang.String outputPrefix,
boolean pairedReads,
java.lang.String namePrefix,
boolean includeNonPfReads)
Constructor
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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
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Modifier and Type | Method and Description |
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void |
writeBfqFiles()
Writes the binary fastq file(s) to the output directory
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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)
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(java.io.File bamFile, java.lang.String outputPrefix, boolean pairedReads, java.lang.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