Package ngs

Interface Fragment

All Known Subinterfaces:
Alignment, AlignmentIterator, FragmentIterator, Read, ReadIterator
public interface Fragment
Represents an NGS biological fragment

  • Method Details

    • getFragmentId

      String getFragmentId() throws ErrorMsg
      getFragmentId
      Returns:
      the unique ID of the fragment
      Throws:
      ErrorMsg - upon an error accessing data

    • getFragmentBases

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

    • getFragmentBases

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

    • getFragmentBases

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

    • getFragmentQualities

      String getFragmentQualities() throws ErrorMsg
      getFragmentQualities using ASCII offset of 33
      Returns:
      phred quality values for the whole fragment
      Throws:
      ErrorMsg - upon an error accessing data

    • getFragmentQualities

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

    • getFragmentQualities

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

    • isPaired

      boolean isPaired() throws ErrorMsg
      isPaired
      Returns:
      true if fragment has a mate
      Throws:
      ErrorMsg - upon an error accessing data

    • isAligned

      boolean isAligned() throws ErrorMsg
      check to see if Fragment has alignment data (requires interface 1.1)
      Returns:
      true if Fragment is aligned
      Throws:
      ErrorMsg - if object is invalid or implementation too old