public class CigarUtil
extends java.lang.Object
Constructor and Description |
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CigarUtil() |
Modifier and Type | Method and Description |
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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.
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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.
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public static java.util.List<CigarElement> softClipEndOfRead(int clipFrom, java.util.List<CigarElement> oldCigar)
clipFrom
- 1-based position where the clipping startsoldCigar
- The existing unclipped cigarpublic static void softClip3PrimeEndOfRead(SAMRecord rec, int clipFrom)
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.public static Cigar addSoftClippedBasesToEndsOfCigar(Cigar cigar, boolean negativeStrand, int threePrimeEnd, int fivePrimeEnd)
cigar
- The cigar on which to base the new cigarnegativeStrand
- Whether the read is on the negative strandthreePrimeEnd
- number of soft-clipped bases to add to the 3' end of the readfivePrimeEnd
- number of soft-clipped bases to add to the 5' end of the readpublic static char[] cigarArrayFromElements(java.util.List<CigarElement> cigar)
public static char[] cigarArrayFromString(java.lang.String cigar)
public static java.lang.String cigarStringFromArray(char[] cigar)