Package org.snpeff.binseq

Class DnaAndQualitySequence

java.lang.Object
org.snpeff.binseq.BinarySequence
org.snpeff.binseq.DnaAndQualitySequence
All Implemented Interfaces:
Serializable, Cloneable, Comparable<BinarySequence>
Direct Known Subclasses:
DnaAndQualitySequenceWithId
public class DnaAndQualitySequence extends BinarySequence
Binary packed DNA sequence and base calling quality Notes: - This is designed for short sequences (such as "short reads") - Every base is encoded in 8 bits: - Six bits for the base quality [0 , .. , 63] - Two bits for the base {a, c, g, t} <=> {0, 1, 2, 3} - All bits are stored in an array of 'bytes'
Author:
pcingola
See Also:

  • Constructor Details

    • DnaAndQualitySequence

      public DnaAndQualitySequence(org.biojava.nbio.genome.io.fastq.Fastq fastq)

    • DnaAndQualitySequence

      public DnaAndQualitySequence(String seqStr)

    • DnaAndQualitySequence

      public DnaAndQualitySequence(String seqStr, String qualityStr, org.biojava.nbio.genome.io.fastq.FastqVariant type)

  • Method Details

    • empty

      public static DnaAndQualitySequence empty()

    • compareTo

      public int compareTo(BinarySequence o)

    • getBase

      public char getBase(int index)
      Description copied from class: BinarySequence
      Return the base at position 'index'
      Overrides:
      getBase in class BinarySequence

    • getCode

      public int getCode(int index)
      Description copied from class: BinarySequence
      Return the code at position 'index'
      Specified by:
      getCode in class BinarySequence

    • getCoder

      public Coder getCoder()
      Description copied from class: BinarySequence
      Get sequence encoder & decoder
      Specified by:
      getCoder in class BinarySequence

    • getCodes

      public byte[] getCodes()

    • getQuality

      public String getQuality()
      Get quality string (encoded FastQ-Sanger style)
      Returns:

    • getQuality

      public int getQuality(int index)

    • getSequence

      public String getSequence()
      Description copied from class: BinarySequence
      Get the sequence as a String
      Specified by:
      getSequence in class BinarySequence

    • hashCode

      public int hashCode()
      Specified by:
      hashCode in class BinarySequence

    • indexOf

      public int indexOf(String seq)
      Find the position of 'seq' in this sequence
      Parameters:
      seq - : String to be found
      Returns:
      The position where 'seq' is found or '-1' if not found

    • lastIndexOf

      public int lastIndexOf(String seq)
      Returns the index within this string of the rightmost occurrence of the specified substring

    • length

      public int length()
      Sequence lenth
      Specified by:
      length in class BinarySequence
      Returns:

    • overlap

      public DnaAndQualitySequence overlap(BinarySequence sequence, int start)
      Creates a new sequence by overlapping 'this' and 'sequence' E.g. this.sequence : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOO | other.sequence : | OOOOOOOOOOOOOOOOOOOOOOOOyyyyyyyyyyyyyyyyy| | |start=20 | result : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOOyyyyyyyyyyyyyyyyy| this.sequence : | OOOOOOOOOOOOOOOOOOOOOOOOxxxxxxxxxxxxxxxxxxxx| other.sequence : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOO | |start=-20 | result : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOOxxxxxxxxxxxxxxxxxxxx| Another case is when a sequence is fully included in the other sequence. In this case the result is just a copy of the longest sequence (with the quality updated) E.g. this.sequence : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOO| other.sequence : | OOOOOOOOOOOOOOO | | |start=20 | result : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOO| this.sequence : | OOOOOOOOOOO | other.sequence : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOO| |start=-20 | result : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOO|
      Overrides:
      overlap in class BinarySequence
      Parameters:
      start -
      Returns:
      A new sequence

    • read

      public DnaAndQualitySequence read(DataInputStream dataInStream) throws IOException
      Read data in binary format
      Specified by:
      read in class BinarySequence
      Parameters:
      dataOutStream -
      Throws:
      IOException

    • readDataStream

      protected void readDataStream(DataInputStream dataInStream) throws IOException
      Read data in binary format
      Specified by:
      readDataStream in class BinarySequence
      Parameters:
      dataOutStream -
      Throws:
      IOException

    • reverseWc

      public DnaAndQualitySequence reverseWc()
      Description copied from class: BinarySequence
      Reverse Watson-Cricks complement
      Specified by:
      reverseWc in class BinarySequence

    • set

      public void set(String seqStr)
      Set sequence
      Specified by:
      set in class BinarySequence
      Parameters:
      seqStr -

    • set

      public void set(String seqStr, String qualityStr, org.biojava.nbio.genome.io.fastq.FastqVariant type)
      Set sequence
      Parameters:
      seqStr -

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • write

      public void write(DataOutputStream dataOutStream) throws IOException
      Write data in binary format
      Specified by:
      write in class BinarySequence
      Parameters:
      dataOutStream -
      Throws:
      IOException