public CigarElement(final int length, final CigarOperator operator) { if (length < 0) throw new IllegalArgumentException(String.format("Cigar element being constructed with negative length: %d and operation: %s" , length, operator.name())); this.length = length; this.operator = operator; }
public CigarElement(final int length, final CigarOperator operator) { if (length < 0) throw new IllegalArgumentException(String.format("Cigar element being constructed with negative length: %d and operation: %s" , length, operator.name())); this.length = length; this.operator = operator; }
@Override public void onTraversalDone(Map<Integer, Map<CigarOperator, Long>> result) { GATKReport report = GATKReport.newSimpleReport("Events", "Position", "Event", "Observations"); for (Map.Entry<Integer, Map<CigarOperator, Long>> entry : result.entrySet()) { int position = entry.getKey(); Map<CigarOperator, Long> operatorCount = entry.getValue(); for (Map.Entry<CigarOperator, Long> subEntry: operatorCount.entrySet()) { String operator = subEntry.getKey().name(); Long observations = subEntry.getValue(); report.addRow(position, operator, observations); } } report.print(out); } }
if (op != CigarOperator.S) throw new IllegalStateException("Should never happen: " + op.name()); if (i == 0 || i == cigarElements.size() - 1) { if (ret == null) ret = new ArrayList<SAMValidationError>(); ret.add(new SAMValidationError(SAMValidationError.Type.ADJACENT_INDEL_IN_CIGAR, "No M or N operator between pair of " + op.name() + " operators in CIGAR", readName, recordNumber));
if (op != CigarOperator.S) throw new IllegalStateException("Should never happen: " + op.name()); if (i == 0 || i == cigarElements.size() - 1) { if (ret == null) ret = new ArrayList<SAMValidationError>(); ret.add(new SAMValidationError(SAMValidationError.Type.ADJACENT_INDEL_IN_CIGAR, "No M or N operator between pair of " + op.name() + " operators in CIGAR", readName, recordNumber));
if (op != CigarOperator.S) throw new IllegalStateException("Should never happen: " + op.name()); if (i == 0 || i == cigarElements.size() - 1) { if (ret == null) ret = new ArrayList<SAMValidationError>(); ret.add(new SAMValidationError(SAMValidationError.Type.ADJACENT_INDEL_IN_CIGAR, "No M or N operator between pair of " + op.name() + " operators in CIGAR", readName, recordNumber));