htsjdk.samtools.util

Class CigarUtil

java.lang.Object

htsjdk.samtools.util.CigarUtil

public class CigarUtil
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
CigarUtil()

Method Summary

Modifier and Type	Method and Description
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.
static char[]	cigarArrayFromElements(java.util.List<CigarElement> cigar)
static char[]	cigarArrayFromString(java.lang.String cigar)
static java.lang.String	cigarStringFromArray(char[] cigar)
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.
static java.util.List<CigarElement>	softClipEndOfRead(int clipFrom, java.util.List<CigarElement> oldCigar) adjust the cigar based on adapter clipping.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CigarUtil

public CigarUtil()

Method Detail

softClipEndOfRead

public static java.util.List<CigarElement> softClipEndOfRead(int clipFrom,
                                                             java.util.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(java.util.List<CigarElement> cigar)

cigarArrayFromString

public static char[] cigarArrayFromString(java.lang.String cigar)

cigarStringFromArray

public static java.lang.String cigarStringFromArray(char[] cigar)