Constant Field Values

Contents

picard.analysis.*

picard.arrays.*

picard.cmdline.*

picard.fingerprint.*

picard.illumina.*

  • picard.illumina.parser.MultiTileBclParser 
    Modifier and Type Constant Field Value
    public static final byte MASKING_QUALITY 2
  • picard.illumina.parser.ParameterizedFileUtil 
    Modifier and Type Constant Field Value
    protected static final boolean DefaultSkipEmptyFiles true
    public static final String PER_TILE_PATTERN_STRING "s_(\\d+)_(\\d{1,5})"
  • picard.illumina.parser.ReadStructure 
    Modifier and Type Constant Field Value
    public static final String PARAMETER_DOC "A description of the logical structure of clusters in an Illumina Run, i.e. a description of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of integer/character pairs describing the number of cycles and the type of those cycles (B for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the input data consists of 80 base clusters and we provide a read structure of \"28T8M8B8S28T\" then the sequence may be split up into four reads:\n* read one with 28 cycles (bases) of template\n* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)\n* read three with 8 cycles (bases) of sample barcode\n* 8 cycles (bases) skipped.\n* read four with 28 cycles (bases) of template\nThe skipped cycles would NOT be included in an output SAM/BAM file or in read groups therein."

picard.metrics.*

picard.sam.*

picard.util.*

picard.vcf.*