Package picard.fastq

Class SamToBfqWriter

java.lang.Object
picard.fastq.SamToBfqWriter
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.
  • Constructor Details

    • 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 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
    • SamToBfqWriter

      public SamToBfqWriter(File samFile, String outputPrefix, boolean pairedReads, String namePrefix, boolean includeNonPfReads)
      Constructor
      Parameters:
      samFile - 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 Details

    • writeBfqFiles

      public void writeBfqFiles()
      Writes the binary fastq file(s) to the output directory