Interface Read

All Superinterfaces:
Fragment, FragmentIterator
All Known Subinterfaces:
ReadIterator
public interface Read extends FragmentIterator

  • Field Details

  • Method Details

    • getReadId

      String getReadId() throws ErrorMsg
      getReadId
      Returns:
      the ID-String of the Read
      Throws:
      ErrorMsg - upon an error accessing data

    • getNumFragments

      int getNumFragments() throws ErrorMsg
      getNumFragments
      Returns:
      the number of biological Fragments contained in the read
      Throws:
      ErrorMsg - upon an error accessing data

    • fragmentIsAligned

      boolean fragmentIsAligned(int fragIdx) throws ErrorMsg
      fragmentIsAligned
      Parameters:
      fragIdx - is a zero-based and non-negative fragment index
      Returns:
      true if a fragment is aligned
      Throws:
      ErrorMsg - upon an error accessing data

    • getReadCategory

      int getReadCategory() throws ErrorMsg
      getReadCategory
      Returns:
      the category of the read
      Throws:
      ErrorMsg - upon an error accessing data

    • getReadGroup

      String getReadGroup() throws ErrorMsg
      getReadGroup
      Returns:
      the read-group of the read
      Throws:
      ErrorMsg - upon an error accessing data

    • getReadName

      String getReadName() throws ErrorMsg
      getReadName
      Returns:
      the name of thethe read
      Throws:
      ErrorMsg - upon an error accessing data

    • getReadBases

      String getReadBases() throws ErrorMsg
      getReadBases
      Returns:
      sequence bases
      Throws:
      ErrorMsg - upon an error accessing data

    • getReadBases

      String getReadBases(long offset) throws ErrorMsg, IndexOutOfBoundsException
      getReadBases
      Parameters:
      offset - is zero-based and non-negative
      Returns:
      sequence bases
      Throws:
      ErrorMsg - upon an error accessing data
      IndexOutOfBoundsException - if offset is invalid

    • getReadBases

      String getReadBases(long offset, long length) throws ErrorMsg, IndexOutOfBoundsException
      getReadBases
      Parameters:
      offset - is zero-based and non-negative
      length - must be ≥ 0
      Returns:
      sequence bases
      Throws:
      ErrorMsg - upon an error accessing data
      IndexOutOfBoundsException - if offset/length are invalid

    • getReadQualities

      String getReadQualities() throws ErrorMsg
      getReadQualities
      Returns:
      phred quality values using ASCII offset of 33
      Throws:
      ErrorMsg - upon an error accessing data

    • getReadQualities

      String getReadQualities(long offset) throws ErrorMsg, IndexOutOfBoundsException
      getReadQualities
      Parameters:
      offset - is zero-based and non-negative
      Returns:
      phred quality values using ASCII offset of 33
      Throws:
      ErrorMsg - upon an error accessing data
      IndexOutOfBoundsException - if offset is invalid

    • getReadQualities

      String getReadQualities(long offset, long length) throws ErrorMsg, IndexOutOfBoundsException
      getReadQualities
      Parameters:
      offset - is zero-based and non-negative
      length - must be ≥ 0
      Returns:
      phred quality values using ASCII offset of 33
      Throws:
      ErrorMsg - upon an error accessing data
      IndexOutOfBoundsException - if offset/length are invalid