Examples of picard.PicardException

picard.PicardException
Basic Picard runtime exception that, for now, does nothing much @author Kathleen Tibbetts

        return parser.getFileName();
    }


    protected void validateLane(final int lane) {
        if (lane != getLane()) {
            throw new PicardException("Lane number mismatch: " + lane + " != " + getLane());
        }
    }

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                                               final boolean skipPairsWithNoMateCigar,
                                               final int maxRecordsInRam,
                                               final int blockSize,
                                               final List<File> tmpDirs) throws PicardException {
        if (header.getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
            throw new PicardException(getClass().getName() + " expects the input to be in coordinate sort order.");
        }


        this.header = header;
        backingIterator = new PeekableIterator<SAMRecord>(iterator);
        outputBuffer = new SamRecordTrackingBuffer<SamRecordWithOrdinalAndSetDuplicateReadFlag>(maxRecordsInRam, blockSize, tmpDirs, header, SamRecordWithOrdinalAndSetDuplicateReadFlag.class);


        this.removeDuplicates = removeDuplicates;
        this.skipPairsWithNoMateCigar = skipPairsWithNoMateCigar;
        this.opticalDuplicateFinder = opticalDuplicateFinder;
        toMarkQueue = new MarkQueue(duplicateScoringStrategy);
        libraryIdGenerator = new LibraryIdGenerator(header);


        // Check for supported scoring strategies
        if (duplicateScoringStrategy == ScoringStrategy.SUM_OF_BASE_QUALITIES)
            throw new PicardException("SUM_OF_BASE_QUALITIES not supported as this may cause inconsistencies across ends in a pair.  Please use a different scoring strategy.");


        // set up metrics
        for (final SAMReadGroupRecord readGroup : header.getReadGroups()) {
            final String library = readGroup.getLibrary();
            DuplicationMetrics metrics = libraryIdGenerator.getMetricsByLibrary(library);

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        // Check for sorted order
        if (null != nextRecord && 0 < sortComparator.fileOrderCompare(toReturn, nextRecord)) {
            System.err.print("Previous record: " + toReturn.getSAMString());
            System.err.print("Current record:" + nextRecord.getSAMString());
            throw new PicardException("Records were not found coordinate sort order");
        }


        return toReturn;
    }

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                outputBuffer.setResultState(samRecordWithOrdinal, false); // indicate the present wrapped samRecordWithOrdinal is available for return
                numRecordsWithNoMateCigar++;
                backingIterator.next(); // remove it, since we called backingIterator.peek()
                return true;
            } else {
                throw new PicardException("Read " + record.getReadName() + " was mapped and had a mapped mate, but no mate cigar (\"MC\") tag.");
            }
        }
        return false;
    }

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                ++metrics.UNMAPPED_READS;
            }


            // We should have no more in the queue
            if (!outputBuffer.isEmpty()) {
                throw new PicardException("Encountered unmapped reads at the end of the file, but the alignment start buffer was not empty.");
            }
            return unmappedRecord; // unmapped end of file records can simply be emitted - no need to duplicate mark them
        } else {
            foundUnmappedEOFReads = true;
            // move past all mapped reads

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    private void checkForMinimumDistanceFailure(final ReadEndsForMateCigar current) {
        if (!toMarkQueue.isEmpty()) {
            final ReadEndsForMateCigar other = toMarkQueue.peek();
            if (other.read1ReferenceIndex == current.read1ReferenceIndex && toMarkQueue.getToMarkQueueMinimumDistance() <= other.read1Coordinate - current.read1Coordinate) {
                if (checkCigarForSkips(other.getRecord().getCigar())) {
                    throw new PicardException("Found a samRecordWithOrdinal with sufficiently large code length that we may have\n"
                            + " missed including it in an early duplicate marking iteration.  Alignment contains skipped"
                            + " reference bases (N's). If this is an\n RNAseq aligned bam, please use MarkDuplicates instead,"
                            + " as this tool does not work well with spliced reads.\n Minimum distance set to "
                            + toMarkQueue.getToMarkQueueMinimumDistance() + " but " + (other.read1Coordinate - current.read1Coordinate - 1)
                            + " would be required.\n" + "Record was: " + other.getRecord().getSAMString());
                } else {
                    System.err.print("record #1: " + other.getRecord().getSAMString());
                    System.err.print("record #2: " + current.getRecord().getSAMString());
                    throw new PicardException("Found a samRecordWithOrdinal with sufficiently large clipping that we may have\n"
                            + " missed including it in an early duplicate marking iteration.  Please increase the"
                            + " minimum distance to at least " + (other.read1Coordinate - current.read1Coordinate - 1)
                            + "bp\nto ensure it is considered (was " + toMarkQueue.getToMarkQueueMinimumDistance() + ").\n"
                            + "Record was: " + other.getRecord().getSAMString());
                }

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        }
        return false;
    }


    private void enforceClosed() {
        if (!isClosed) throw new PicardException("Calling a method that assumes the iterator is closed");
    }

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     * @throws PicardException if the records are added out of order
     */
    private void addRecordToTheOutputBuffer(final SamRecordWithOrdinal samRecordWithOrdinal) throws PicardException {
        final int recordReferenceIndex = samRecordWithOrdinal.getRecord().getReferenceIndex();
        if (recordReferenceIndex < referenceIndex) {
            throw new PicardException("Records out of order: " + recordReferenceIndex + " < " + referenceIndex);
        } else if (referenceIndex < recordReferenceIndex) {
            // new reference, so we need to mark duplicates on the current ones
            // NB: we will not miss inter-chromosomal alignments since presumably one end will have been mapped to this chromosome and processed, and we do not need the other end to do so.
            tryPollingTheToMarkQueue(true, null);
            // update genomic coordinate to the next reference index

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     * @return true if we did get at least one record, false otherwise
     */
    private boolean tryPollingTheToMarkQueue(final boolean flush, final ReadEndsForMateCigar current) {
        boolean performedChunkAndMarkTheDuplicates = false;


        if (!flush && null == current) throw new PicardException("Flush cannot be false and current be null");


        if (toMarkQueue.isEmpty()) return false;


        if (!toMarkQueue.isEmpty() && outputBuffer.isEmpty()) {
            throw new PicardException("0 < toMarkQueue && outputBuffer.isEmpty()");
        }


        /**
         * Try to poll the toMarkQueue.  If we are flushing all the records from it, just do so until empty.  Otherwise, we need to
         * make sure we only poll those a certain distance away from current.

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        this.referenceFasta = referenceFasta;


        this.refSeq = new ReferenceSequenceFileWalker(referenceFasta);
        this.sequenceDictionary = refSeq.getSequenceDictionary();
        if (this.sequenceDictionary == null) {
            throw new PicardException("No sequence dictionary found for " + referenceFasta.getAbsolutePath() +
                    ".  Use CreateSequenceDictionary.jar to create a sequence dictionary.");
        }


        this.clipAdapters = clipAdapters;
        this.bisulfiteSequence = bisulfiteSequence;

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