Package org.broadinstitute.gatk.utils.clipping

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


                    //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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