Package picard.util

Class AdapterMarker

java.lang.Object
picard.util.AdapterMarker
public class AdapterMarker extends Object
Store one or more AdapterPairs to use to mark adapter sequence of SAMRecords. This is a very compute-intensive process, so this class implements two heuristics to reduce computation: - Adapter sequences are truncated, and then any adapter pairs that become identical after truncation are collapsed into a single pair. - After a specified number of reads with adapter sequence has been seen, prune the list of adapter pairs to include only the most frequently seen adapters. For a flowcell, there should only be a single adapter pair found. Note that the AdapterPair object returned by all the adapterTrim* methods will not be one of the original AdapterPairs passed to the ctor, but rather will be one of the truncated copies.

  • Field Details

    • DEFAULT_ADAPTER_LENGTH

      public static final int DEFAULT_ADAPTER_LENGTH
      See Also:

    • DEFAULT_PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN

      public static final int DEFAULT_PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN
      See Also:

    • DEFAULT_NUM_ADAPTERS_TO_KEEP

      public static final int DEFAULT_NUM_ADAPTERS_TO_KEEP
      See Also:

  • Constructor Details

    • AdapterMarker

      public AdapterMarker(AdapterPair... originalAdapters)
      Truncates adapters to DEFAULT_ADAPTER_LENGTH
      Parameters:
      originalAdapters - These should be in order from longest invalid input: '&' most likely to shortest invalid input: '&' least likely.

    • AdapterMarker

      public AdapterMarker(int adapterLength, AdapterPair... originalAdapters)
      Parameters:
      adapterLength - Truncate adapters to this length.
      originalAdapters - These should be in order from longest invalid input: '&' most likely to shortest invalid input: '&' least likely.

  • Method Details

    • getNumAdaptersToKeep

      public int getNumAdaptersToKeep()

    • setNumAdaptersToKeep

      public AdapterMarker setNumAdaptersToKeep(int numAdaptersToKeep)
      After seeing the thresholdForSelectingAdapters number of adapters, keep up to this many of the original adapters.

    • getThresholdForSelectingAdaptersToKeep

      public int getThresholdForSelectingAdaptersToKeep()

    • setThresholdForSelectingAdaptersToKeep

      public AdapterMarker setThresholdForSelectingAdaptersToKeep(int thresholdForSelectingAdaptersToKeep)
      When this number of adapters have been matched, discard the least-frequently matching ones.
      Parameters:
      thresholdForSelectingAdaptersToKeep - set to -1 to never discard any adapters.

    • getMinSingleEndMatchBases

      public int getMinSingleEndMatchBases()

    • setMinSingleEndMatchBases

      public AdapterMarker setMinSingleEndMatchBases(int minSingleEndMatchBases)
      Parameters:
      minSingleEndMatchBases - When marking a single-end read, adapter must match at least this many bases.

    • getMinPairMatchBases

      public int getMinPairMatchBases()

    • setMinPairMatchBases

      public AdapterMarker setMinPairMatchBases(int minPairMatchBases)
      Parameters:
      minPairMatchBases - When marking a paired-end read, adapter must match at least this many bases.

    • getMaxSingleEndErrorRate

      public double getMaxSingleEndErrorRate()

    • setMaxSingleEndErrorRate

      public AdapterMarker setMaxSingleEndErrorRate(double maxSingleEndErrorRate)
      Parameters:
      maxSingleEndErrorRate - For single-end read, no more than this fraction of the bases that align with the adapter can mismatch the adapter and still be considered an adapter match.

    • getMaxPairErrorRate

      public double getMaxPairErrorRate()

    • setMaxPairErrorRate

      public AdapterMarker setMaxPairErrorRate(double maxPairErrorRate)
      Parameters:
      maxPairErrorRate - For paired-end read, no more than this fraction of the bases that align with the adapter can mismatch the adapter and still be considered an adapter match.

    • adapterTrimIlluminaSingleRead

      public AdapterPair adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read)

    • findAdapterPairAndIndexForSingleRead

      public htsjdk.samtools.util.Tuple<AdapterPair,Integer> findAdapterPairAndIndexForSingleRead(byte[] read, int templateIndex)
      Return the adapter to be trimmed from a read represented as an array of bytes[]
      Parameters:
      read - The byte array of read data
      templateIndex - The paired index of the reads (1 or 2, 1 for single ended reads)
      Returns:
      The adapter pair that matched the read and its index in the read.

    • adapterTrimIlluminaPairedReads

      public AdapterPair adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2)

    • adapterTrimIlluminaSingleRead

      public AdapterPair adapterTrimIlluminaSingleRead(htsjdk.samtools.SAMRecord read, int minMatchBases, double maxErrorRate)
      Overrides defaults for minMatchBases and maxErrorRate

    • findAdapterPairAndIndexForSingleRead

      public htsjdk.samtools.util.Tuple<AdapterPair,Integer> findAdapterPairAndIndexForSingleRead(byte[] read, int minMatchBases, double maxErrorRate, int templateIndex)
      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)
      Returns:
      The adapter pair that matched the read and its index in the read or null.

    • adapterTrimIlluminaPairedReads

      public AdapterPair adapterTrimIlluminaPairedReads(htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2, int minMatchBases, double maxErrorRate)
      Overrides defaults for minMatchBases and maxErrorRate