public class BamToBfqWriter extends Object
Constructor and Description |
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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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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