Examples of picard.PicardException

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

            if (printStream.checkError()) {
                return 1;
            }
            return 0;
        } catch (IOException e) {
            throw new PicardException("Exception writing SAM text", e);
        }
    }

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            // Do the clipping one way for PE and another for SE reads
            if (rec.getReadPairedFlag()) {
                // Assert that the input file is in query name order only if we see some PE reads
                if (order != SAMFileHeader.SortOrder.queryname) {
                    throw new PicardException("Input BAM file must be sorted by queryname");
                }


                if (rec2 == null) throw new PicardException("Missing mate pair for paired read: " + rec.getReadName());
                rec2.setAttribute(ReservedTagConstants.XT, null);


                // Assert that we did in fact just get two mate pairs
                if (!rec.getReadName().equals(rec2.getReadName())){
                    throw new PicardException("Adjacent reads expected to be mate-pairs have different names: " +
                            rec.getReadName() + ", " + rec2.getReadName());
                }


                // establish which of pair is first and which second
                final SAMRecord first, second;


                if (rec.getFirstOfPairFlag() && rec2.getSecondOfPairFlag()){
                    first = rec;
                    second = rec2;
                }
                else if (rec.getSecondOfPairFlag() && rec2.getFirstOfPairFlag()) {
                    first = rec2;
                    second = rec;
                }
                else {
                    throw new PicardException("Two reads with same name but not correctly marked as 1st/2nd of pair: " + rec.getReadName());
                }


                adapterMarker.adapterTrimIlluminaPairedReads(first, second);
            }
            else {

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                final SAMSequenceRecord sequenceRecord = header.getSequenceDictionary().getSequence(sequenceName);


                // Do some validation
                if (null == sequenceRecord) {
                    throw new PicardException(String.format("Sequence '%s' was not found in the sequence dictionary", sequenceName));
                }
                else if (start < 1) {
                    throw new PicardException(String.format("Start on sequence '%s' was less than one: %d", sequenceName, start));
                }
                else if (sequenceRecord.getSequenceLength() < start) {
                    throw new PicardException(String.format("Start on sequence '%s' was past the end: %d < %d", sequenceName, sequenceRecord.getSequenceLength(), start));
                }
                else if (end < 1) {
                    throw new PicardException(String.format("End on sequence '%s' was less than one: %d", sequenceName, end));
                }
                else if (sequenceRecord.getSequenceLength() < end) {
                    throw new PicardException(String.format("End on sequence '%s' was past the end: %d < %d", sequenceName, sequenceRecord.getSequenceLength(), end));
                }
                else if (end < start - 1) {
                    throw new PicardException(String.format("On sequence '%s', end < start-1: %d <= %d", sequenceName, end, start));
                }


                final Interval interval = new Interval(sequenceName, start, end, bedFeature.getStrand() == Strand.POSITIVE, name);
                intervalList.add(interval);

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                allLaneCounts.addIlluminaMetricCounts(counts);
            }
            if (! barcodeToMetricCounts.keySet().contains("")) allLaneCounts.addMetricsToFile(file);  // detect non-indexed case
            file.write(OUTPUT);
        } catch (final Exception ex) {
            throw new PicardException("Error writing output file " + OUTPUT.getPath(), ex);
        }
    }

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    }


    private static void createDirectoryOrFail(final File directory) {
        if (!directory.exists()) {
            if (!directory.mkdir()) {
                throw new PicardException("Unable to create directory: " + directory.getAbsolutePath());
            }
        }
    }

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            byte ret = buf.get();
            tmpFile.delete();
            alreadyCalled = true;
            return ret;
        } catch (IOException e) {
            throw new PicardException("IOException", e);
        }


    }

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    private Set<String> findAndFilterExpectedColumns(final Set<String> actualCols, final Set<String> expectedCols) {
        final Set<String> missingColumns = new HashSet<String>(expectedCols);
        missingColumns.removeAll(actualCols);


        if (missingColumns.size() > 0) {
            throw new PicardException(String.format(
                    "LIBRARY_PARAMS file %s is missing the following columns: %s.",
                    LIBRARY_PARAMS.getAbsolutePath(), StringUtil.join(", ", missingColumns
            )));
        }

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    private void checkRgTagColumns(final Set<String> rgTagColumns) {
        final Set<String> forbiddenHeaders = buildSamHeaderParameters(null).keySet();
        forbiddenHeaders.retainAll(rgTagColumns);


        if (forbiddenHeaders.size() > 0) {
            throw new PicardException("Illegal ReadGroup tags in library params(barcode params) file(" + LIBRARY_PARAMS.getAbsolutePath() + ") Offending headers = " + StringUtil.join(", ", forbiddenHeaders));
        }


        for (final String column : rgTagColumns) {
            if (column.length() > 2) {
                throw new PicardException("Column label (" + column + ") unrecognized.  Library params(barcode params) can only contain the columns " +
                        "(OUTPUT, LIBRARY_NAME, SAMPLE_ALIAS, BARCODE, BARCODE_<X> where X is a positive integer) OR two letter RG tags!");
            }
        }
    }

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            if (libraryParamsParser.hasColumn("BARCODE")) {
                barcodeColumnLabels.add("BARCODE");
            } else if (libraryParamsParser.hasColumn("BARCODE_1")) {
                barcodeColumnLabels.add("BARCODE_1");
            } else {
                throw new PicardException("LIBRARY_PARAMS(BARCODE_PARAMS) file " + LIBRARY_PARAMS + " does not have column BARCODE or BARCODE_1.");
            }
        } else {
            for (int i = 1; i <= readStructure.barcodes.length(); i++) {
                barcodeColumnLabels.add("BARCODE_" + i);
            }
        }


        expectedColumnLabels.addAll(barcodeColumnLabels);
        final Set<String> rgTagColumns = findAndFilterExpectedColumns(libraryParamsParser.columnLabels(), expectedColumnLabels);
        checkRgTagColumns(rgTagColumns);


        for (final TabbedTextFileWithHeaderParser.Row row : libraryParamsParser) {
            List<String> barcodeValues = null;


            if (barcodeColumnLabels.size() > 0) {
                barcodeValues = new ArrayList<String>();
                for (final String barcodeLabel : barcodeColumnLabels) {
                    barcodeValues.add(row.getField(barcodeLabel));
                }
            }


            final String key = (barcodeValues == null || barcodeValues.contains("N")) ? null : StringUtil.join("", barcodeValues);
            if (barcodeSamWriterMap.containsKey(key)) {    //This will catch the case of having more than 1 line in a non-barcoded LIBRARY_PARAMS file
                throw new PicardException("Row for barcode " + key + " appears more than once in LIBRARY_PARAMS or BARCODE_PARAMS file " +
                        LIBRARY_PARAMS);
            }


            final Map<String, String> samHeaderParams = buildSamHeaderParameters(barcodeValues);


            for (final String tagName : rgTagColumns) {
                samHeaderParams.put(tagName, row.getField(tagName));
            }


            final SAMFileWriterWrapper writer = buildSamFileWriter(new File(row.getField("OUTPUT")),
                    row.getField("SAMPLE_ALIAS"), row.getField("LIBRARY_NAME"), samHeaderParams);
            barcodeSamWriterMap.put(key, writer);
        }
        if (barcodeSamWriterMap.isEmpty()) {
            throw new PicardException("LIBRARY_PARAMS(BARCODE_PARAMS) file " + LIBRARY_PARAMS + " does have any data rows.");
        }
        libraryParamsParser.close();
    }

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                bestQuality = quality;
            }
        }
        final int qualityAsCharacter = bestQuality + SolexaQualityConverter.SOLEXA_ADDEND;
        if (qualityAsCharacter > 255) {
            throw new PicardException("Quality too large: " + bestQuality);
        }
        return (byte)(qualityAsCharacter & 0xff);
    }

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