Package picard.fastq

Class 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 Detail

      • 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 Detail

      • writeBfqFiles

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