Package picard.fastq
Class SamToBfqWriter
- java.lang.Object
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- picard.fastq.SamToBfqWriter
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- Direct Known Subclasses:
BamToBfqWriter
public class SamToBfqWriter extends Object
Class to take unmapped reads in SAM/BAM/CRAM 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 file having all paired reads together in order.
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Constructor Summary
Constructors Constructor Description SamToBfqWriter(File samFile, File referenceSequence, String outputPrefix, Integer total, Integer chunk, boolean pairedReads, String namePrefix, boolean includeNonPfReads, boolean clipAdapters, Integer basesToWrite)
ConstructorSamToBfqWriter(File samFile, String outputPrefix, boolean pairedReads, String namePrefix, boolean includeNonPfReads)
Constructor
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
writeBfqFiles()
Writes the binary fastq file(s) to the output directory
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Constructor Detail
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SamToBfqWriter
public SamToBfqWriter(File samFile, File referenceSequence, String outputPrefix, Integer total, Integer chunk, boolean pairedReads, String namePrefix, boolean includeNonPfReads, boolean clipAdapters, Integer basesToWrite)
Constructor- Parameters:
samFile
- 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 attribute
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SamToBfqWriter
public SamToBfqWriter(File samFile, String outputPrefix, boolean pairedReads, String namePrefix, boolean includeNonPfReads)
Constructor- Parameters:
samFile
- 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
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