Package picard.util

Class ClippingUtility

java.lang.Object
picard.util.ClippingUtility

public class ClippingUtility extends Object
Utilities to clip the adapter sequence from a SAMRecord read
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final double
    The default value used for the maximum error rate when matching read bases to clippable sequence.
    static final double
    The default value used for the maximum error rate when matching paired end read bases to clippable sequence.
    static final int
    The default value used for the minimum number of contiguous bases to match against.
    static final int
    The default value used for the minimum number of contiguous bases to match against in a paired end read
    static final int
    The value returned by methods returning int when no match is found.
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Modifier and Type
    Method
    Description
    adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, int minMatchBases, double maxErrorRate, AdapterPair... adapters)
    Invokes adapterTrimIlluminaRead with explicit parameters for a pair of reads.
    static String
    adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, AdapterPair adapters)
    Deprecated.
    Use the varargs version.
    adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, AdapterPair... adapters)
    Invokes adapterTrimIlluminaPairedReads with default less stringent parameters for a pair of reads.
    static String
    adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, AdapterPair adapters, int minMatchBases, double maxErrorRate)
    Deprecated.
    Use the varargs version.
    adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, int minMatchBases, double maxErrorRate, AdapterPair... adapters)
    Invokes adapterTrimIlluminRead with explicit matching thresholds for a single read.
    static void
    adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, AdapterPair adapter)
    Deprecated.
    Use the varargs version.
    adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, AdapterPair... adapters)
    Invokes adapterTrimIlluminRead with default parameters for a single read.
    static void
    adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, AdapterPair adapter, int minMatchBases, double maxErrorRate)
    Deprecated.
    Use the varargs version.
    static htsjdk.samtools.util.Tuple<AdapterPair,Integer>
    findAdapterPairAndIndexForSingleRead(byte[] read, int minMatchBases, double maxErrorRate, int templateIndex, AdapterPair... adapters)
    Return the adapter to be trimmed from a read represented as an array of bytes[]
    static int
    findIndexOfClipSequence(byte[] read, byte[] adapterSequence, int minMatch, double maxErrorRate)
    Finds the first index of the adapterSequence sequence in the read sequence requiring at least minMatch bases of pairwise alignment with a maximum number of errors dictated by maxErrorRate.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Field Details

    • MIN_MATCH_BASES

      public static final int MIN_MATCH_BASES
      The default value used for the minimum number of contiguous bases to match against.
      See Also:
    • MIN_MATCH_PE_BASES

      public static final int MIN_MATCH_PE_BASES
      The default value used for the minimum number of contiguous bases to match against in a paired end read
      See Also:
    • MAX_ERROR_RATE

      public static final double MAX_ERROR_RATE
      The default value used for the maximum error rate when matching read bases to clippable sequence.
      See Also:
    • MAX_PE_ERROR_RATE

      public static final double MAX_PE_ERROR_RATE
      The default value used for the maximum error rate when matching paired end read bases to clippable sequence.
      See Also:
    • NO_MATCH

      public static final int NO_MATCH
      The value returned by methods returning int when no match is found.
      See Also:
  • Constructor Details

    • ClippingUtility

      public ClippingUtility()
  • Method Details

    • adapterTrimIlluminaSingleRead

      public static void adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, AdapterPair adapter)
      Deprecated.
      Use the varargs version. This no longer returns a warning string..
    • adapterTrimIlluminaSingleRead

      public static void adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, AdapterPair adapter, int minMatchBases, double maxErrorRate)
      Deprecated.
      Use the varargs version. This no longer returns a warning string..
    • adapterTrimIlluminaSingleRead

      public static AdapterPair adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, AdapterPair... adapters)
      Invokes adapterTrimIlluminRead with default parameters for a single read. If the read is a negative strand, its bases will be reverse complemented Simpler, more common of two overloads. Accepts multiple adapters and tries them all until it finds the first one that matches.
      Parameters:
      read - SAM/BAM read to trim
      adapters - which adapters to try to use (indexed, paired_end, or single_end)
      Returns:
      AdapterPair the AdapterPair matched, or null
    • adapterTrimIlluminaSingleRead

      public static AdapterPair adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, int minMatchBases, double maxErrorRate, AdapterPair... adapters)
      Invokes adapterTrimIlluminRead with explicit matching thresholds for a single read. If the read is a negative strand, a copy of its bases will be reverse complemented. More general form of the two overloads. Accepts multiple adapters and tries them all until it finds the first one that matches.
      Parameters:
      read - SAM/BAM read to trim
      minMatchBases - minimum number of contiguous bases to match against in a read
      maxErrorRate - maximum error rate when matching read bases
      adapters - which adapters to try (indexed, paired_end, or single_end)
      Returns:
      AdapterPair the AdapterPair matched, or null
    • findAdapterPairAndIndexForSingleRead

      public static htsjdk.samtools.util.Tuple<AdapterPair,Integer> findAdapterPairAndIndexForSingleRead(byte[] read, int minMatchBases, double maxErrorRate, int templateIndex, AdapterPair... adapters)
      Return the adapter to be trimmed from a read represented as an array of bytes[]
      Parameters:
      read - The byte array of read data
      minMatchBases - The minimum number of base matches required for adapter matching
      maxErrorRate - The maximum error rate allowed for adapter matching
      templateIndex - The paired index of the reads (1 or 2, 1 for single ended reads)
      adapters - The set of adapters to search for
      Returns:
      The adapter pair that matched the read and its index in the read or null
    • adapterTrimIlluminaPairedReads

      public static String adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, AdapterPair adapters)
      Deprecated.
      Use the varargs version. This no longer returns a warning string..
    • adapterTrimIlluminaPairedReads

      public static String adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, AdapterPair adapters, int minMatchBases, double maxErrorRate)
      Deprecated.
      Use the varargs version. This no longer returns a warning string..
    • adapterTrimIlluminaPairedReads

      public static AdapterPair adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, AdapterPair... adapters)
      Invokes adapterTrimIlluminaPairedReads with default less stringent parameters for a pair of reads. If the read is a negative strand, its bases will be reverse complemented Simpler, more common of two overloads.
      Parameters:
      read1 - first read of the pair
      read2 - second read of the pair
      adapters - which adapters to use (indexed, paired_end, or single_end, nextera), attempted in order
      Returns:
      int number of bases trimmed
    • adapterTrimIlluminaPairedReads

      public static AdapterPair adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, int minMatchBases, double maxErrorRate, AdapterPair... adapters)
      Invokes adapterTrimIlluminaRead with explicit parameters for a pair of reads. More general form of two overloads. Returns a warning string when the trim positions found differed for each read.
      Parameters:
      read1 - first read of the pair. If read1 is a negative strand, a copy of its bases will be reverse complemented.
      read2 - second read of the pair. If read2 is a negative strand, a copy of its bases will be reverse complemented
      minMatchBases - minimum number of contiguous bases to match against in a read
      maxErrorRate - maximum error rate when matching read bases
      adapters - which adapters to use (indexed, paired_end, or single_end, nextera), attempted in order
      Returns:
      int number of bases trimmed
    • findIndexOfClipSequence

      public static int findIndexOfClipSequence(byte[] read, byte[] adapterSequence, int minMatch, double maxErrorRate)
      Finds the first index of the adapterSequence sequence in the read sequence requiring at least minMatch bases of pairwise alignment with a maximum number of errors dictated by maxErrorRate.
      Parameters:
      read -