Package picard.util

Class IlluminaUtil

java.lang.Object
picard.util.IlluminaUtil
public class IlluminaUtil extends Object
Misc utilities for working with Illumina specific files and data

  • Field Details

  • Constructor Details

    • IlluminaUtil

      public IlluminaUtil()

  • Method Details

    • getTileFromReadName

      public static Integer getTileFromReadName(String readName)
      Parse the tile # from the read name. If we find that there are other elements needed from the read name, it might be a good idea to put makeReadName() and various get..() methods into a new class.
      Parameters:
      readName - As produced by IlluminaUtil.makeReadName()
      Returns:
      tile number, or null if read name is not in correct format.

    • makePhredBinaryFromSolexaQualityAscii_1_3

      public static byte[] makePhredBinaryFromSolexaQualityAscii_1_3(String solexaQualities)
      Convert from Solexa-scaled ASCII qualities to Phred-scaled binary. The only difference is Solexa qualities have 64 added to the phred binary to make them printable.
      Parameters:
      solexaQualities - Printable ASCII qualities.
      Returns:
      binary Phred-scaled qualities.

    • makePhredBinaryFromSolexaQualityAscii_1_3

      public static byte[] makePhredBinaryFromSolexaQualityAscii_1_3(String solexaQualities, int offset, int length)
      Convert from Solexa-scaled ASCII qualities to Phred-scaled binary. The only difference is Solexa qualities have 64 added to the phred binary to make them printable.
      Parameters:
      solexaQualities - Printable ASCII qualities.
      offset - Character at which to start conversion.
      length - Number of characters to convert.
      Returns:
      binary Phred-scaled qualities.

    • convertSolexaQualityAscii_1_1_ToPhredBinary

      public static void convertSolexaQualityAscii_1_1_ToPhredBinary(byte[] solexaQualities)
      Converts from Solexa ASCII to Phred binary in place. These are the older-style qualities rather than Phred qualities with a different addend to make them printable.

    • getSolexaQualityCharFromFourQualities

      public static byte getSolexaQualityCharFromFourQualities(String[] qualities, int cycleNumber, htsjdk.samtools.util.FormatUtil formatter)
      Get a Solexa ASCII quality value from an array of strings that are integer qualities in this order: [cycle-1-A, cycle-1-C, cycle-1-G, cycle-1-T, cycle-2-A, ...]. The best quality from the 4 qualities for the cycle is found, and then it is ASCII-ized by adding 64.
      Parameters:
      qualities - Array of integer quality strings.
      cycleNumber - Which cycle to get quality for.
      formatter - For converting decimal strings to ints.
      Returns:
      best quality for the given cycle.
      Throws:
      PicardException - if the best quality ASCII value is > 255.

    • barcodeSeqsToString

      public static String barcodeSeqsToString(List<String> barcodes)
      Concatenates all the barcode sequences with BARCODE_DELIMITER
      Parameters:
      barcodes -
      Returns:
      A single string representation of all the barcodes

    • barcodeSeqsToString

      public static String barcodeSeqsToString(String[] barcodes)
      Concatenates all the barcode sequences with BARCODE_DELIMITER
      Parameters:
      barcodes -
      Returns:
      A single string representation of all the barcodes

    • barcodeSeqsToString

      public static String barcodeSeqsToString(byte[][] barcodes)
      Concatenates all the barcode sequences with BARCODE_DELIMITER
      Parameters:
      barcodes -
      Returns:
      A single string representation of all the barcodes

    • stringSeqsToString

      public static String stringSeqsToString(String[] barcodes, String delim)

    • byteArrayToString

      public static String byteArrayToString(byte[][] barcodes, String delim)
      Concatenates all the barcode sequences with BARCODE_DELIMITER
      Parameters:
      barcodes -
      Returns:
      A single string representation of all the barcodes