Package htsjdk.samtools.util

Class CigarUtil

java.lang.Object
htsjdk.samtools.util.CigarUtil
public class CigarUtil extends Object

  • Constructor Details

    • CigarUtil

      public CigarUtil()

  • Method Details

    • clipEndOfRead

      public static List<CigarElement> clipEndOfRead(int clipFrom, List<CigarElement> oldCigar, CigarOperator clippingOperator)
      Adjust the cigar based on adapter clipping. TODO: If there is hard clipping at the end of the input CIGAR, it is lost. It should not be. *
      Parameters:
      clipFrom - 1-based position where the clipping starts
      oldCigar - The existing unclipped cigar
      clippingOperator - Type of clipping to use, either soft or hard. If non-clipping operator is used an exception is thrown
      Returns:
      New adjusted list of cigar elements

    • softClipEndOfRead

      public static List<CigarElement> softClipEndOfRead(int clipFrom, List<CigarElement> oldCigar)
      Adjust the cigar based on adapter clipping
      Parameters:
      clipFrom - 1-based position where the clipping starts
      oldCigar - The existing unclipped cigar
      Returns:
      New adjusted list of cigar elements

    • softClip3PrimeEndOfRead

      public static void softClip3PrimeEndOfRead(SAMRecord rec, int clipFrom)
      Adjust the cigar of rec based on adapter clipping using soft-clipping
      Parameters:
      clipFrom - 1-based position where the soft-clipping starts

    • clip3PrimeEndOfRead

      public static void clip3PrimeEndOfRead(SAMRecord rec, int clipFrom, CigarOperator clippingOperator)
      Adds a soft- or hard-clip, based on clipFrom and clippingOperator, to the SAM record's existing cigar and, for negative strands, also adjusts the SAM record's start position. If clipping changes the number of unclipped bases, the the NM, MD, and UQ tags will be invalidated. Clips the end of the read as the read came off the sequencer.
      Parameters:
      rec - SAMRecord to clip
      clipFrom - Position to clip from
      clippingOperator - Type of clipping to use, either soft or hard. If non-clipping operator is used an exception is thrown

    • addClippedBasesToEndsOfCigar

      public static Cigar addClippedBasesToEndsOfCigar(Cigar cigar, boolean negativeStrand, int threePrimeEnd, int fivePrimeEnd, CigarOperator clippingOperator)
      Adds additional soft-clipped bases at the 3' and/or 5' end of the cigar. Does not change the existing cigar except to merge the newly added soft-clipped bases if the element at the end of the cigar being modified is also a soft-clip.
      Parameters:
      cigar - The cigar on which to base the new cigar
      negativeStrand - Whether the read is on the negative strand
      threePrimeEnd - number of soft-clipped bases to add to the 3' end of the read
      fivePrimeEnd - number of soft-clipped bases to add to the 5' end of the read
      clippingOperator - Type of clipping to use, either soft or hard. If non-clipping operator is used an exception is thrown

    • addSoftClippedBasesToEndsOfCigar

      public static Cigar addSoftClippedBasesToEndsOfCigar(Cigar cigar, boolean negativeStrand, int threePrimeEnd, int fivePrimeEnd)
      Adds additional soft-clipped bases at the 3' and/or 5' end of the cigar. Does not change the existing cigar except to merge the newly added soft-clipped bases if the element at the end of the cigar being modified is also a soft-clip.
      Parameters:
      cigar - The cigar on which to base the new cigar
      negativeStrand - Whether the read is on the negative strand
      threePrimeEnd - number of soft-clipped bases to add to the 3' end of the read
      fivePrimeEnd - number of soft-clipped bases to add to the 5' end of the read
      Returns:
      New cigar with additional soft-clipped bases

    • cigarArrayFromElements

      public static char[] cigarArrayFromElements(List<CigarElement> cigar)

    • cigarArrayFromString

      public static char[] cigarArrayFromString(String cigar)

    • cigarStringFromArray

      public static String cigarStringFromArray(char[] cigar)