Package htsjdk.samtools.util

Class CigarUtil

  • public class CigarUtil
extends Object

    • Constructor Detail

      • CigarUtil

        public CigarUtil()

    • Method Detail

      • softClipEndOfRead

        public static List<CigarElement> softClipEndOfRead​(int clipFrom,
                                                   List<CigarElement> oldCigar)
        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
        Returns:
        New adjusted list of cigar elements

      • softClip3PrimeEndOfRead

        public static void softClip3PrimeEndOfRead​(SAMRecord rec,
                                           int clipFrom)
        Adds a soft-clip, based on clipFrom, to the SAM record's existing cigar and, for negative strands, also adjusts the SAM record's start position. Soft clips the end of the read as the read came off the sequencer.

      • 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

      • cigarArrayFromElements

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

      • cigarArrayFromString

        public static char[] cigarArrayFromString​(String cigar)

      • cigarStringFromArray

        public static String cigarStringFromArray​(char[] cigar)