Examples of org.broadinstitute.gatk.utils.clipping.ClippingOp$CigarShift

Package org.broadinstitute.gatk.utils.clipping

Examples of org.broadinstitute.gatk.utils.clipping.ClippingOp$CigarShift

org.broadinstitute.gatk.utils.clipping.ClippingOp
Represents a clip on a read. It has a type (see the enum) along with a start and stop in the bases of the read, plus an option extraInfo (useful for carrying info where needed).
Also holds the critical apply function that actually execute the clipping operation on a provided read, according to the wishes of the supplied ClippingAlgorithm enum.

                    //System.out.printf("Matching %s against %s/%s => %b%n", bases, stc.seq, stc.revSeq, found);
                    if (found) {
                        int start = match.start();
                        int stop = match.end() - 1;
                        //ClippingOp op = new ClippingOp(ClippingOp.ClippingType.MATCHES_CLIP_SEQ, start, stop, stc.seq);
                        ClippingOp op = new ClippingOp(start, stop);
                        clipper.addOp(op);
                        data.incSeqClippedBases(stc.seq, op.getLength());
                    }
                }
            }
            clipper.setData(data);
        }

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                    Pair<Integer, Integer> startStop = strandAwarePositions(read, cycleStart, cycleStop);
                    int start = startStop.first;
                    int stop = startStop.second;


                    //ClippingOp op = new ClippingOp(ClippingOp.ClippingType.WITHIN_CLIP_RANGE, start, stop, null);
                    ClippingOp op = new ClippingOp(start, stop);
                    clipper.addOp(op);
                    data.incNRangeClippedBases(op.getLength());
                }
            }
            clipper.setData(data);
        }
    }

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        if (clipPoint != -1) {
            int start = read.getReadNegativeStrandFlag() ? 0 : clipPoint;
            int stop = read.getReadNegativeStrandFlag() ? clipPoint : readLen - 1;
            //clipper.addOp(new ClippingOp(ClippingOp.ClippingType.LOW_Q_SCORES, start, stop, null));
            ClippingOp op = new ClippingOp(start, stop);
            clipper.addOp(op);
            data.incNQClippedBases(op.getLength());
        }
        clipper.setData(data);
    }

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org.broadinstitute.gatk.utils.exceptions.UserException

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