Examples of picard.PicardException

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

     * Either set this value if not already set, or if already set, throw an exception if new value != current value.
     */
    public void setOrCheckY(final int y) {
        if (yIsSet()) {
            if (this.y != y) {
                throw new PicardException("Y value mismatch for " + this + " : " + this.y + " != " + y);
            }
        } else {
            this.y = y;
        }
    }

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     */
    public void setOrCheckPf(final boolean pf) {
        if (this.pf == null) {
            this.pf = pf;
        } else if (this.pf != pf) {
            throw new PicardException("PF value mismatch for " + this + " : ");
        }
    }

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                    CHART_OUTPUT.getAbsolutePath(),
                    INPUT.getName(),
                    this.plotSubtitle);


            if (rResult != 0) {
                throw new PicardException("R script qualityScoreDistribution.R failed with return code " + rResult);
            }
        }
    }

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                this.out.writeInt(val.read1.length);
                this.out.write(val.read1);
                this.out.writeInt(val.read2.length);
                this.out.write(val.read2);
            } catch (IOException ioe) {
                throw new PicardException("Error write out read pair.", ioe);
            }
        }

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                val.y = this.in.readShort();


                int length = this.in.readInt();
                val.read1 = new byte[length];
                if (this.in.read(val.read1) != length) {
                    throw new PicardException("Could not read " + length + " bytes from temporary file.");
                }


                length = this.in.readInt();
                val.read2 = new byte[length];
                if (this.in.read(val.read2) != length) {
                    throw new PicardException("Could not read " + length + " bytes from temporary file.");
                }


                return val;
            } catch (IOException ioe) {
                throw new PicardException("Exception reading read pair.", ioe);
            }
        }

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            else {
                return 0;
            }
        }
        catch (IOException ioe) {
            throw new PicardException("Exception reading terminator block of file: " + INPUT.getAbsolutePath());
        }
    }

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                ++outputCycleIndex;
            }
        }


        if(outputCycleIndex != outputCycles.length) {
            throw new PicardException("Error in read structure outputCycles (" + StringUtil.intValuesToString(outputCycles) + ") and total cycles (" + totalCycles + ") OutputCycleIndex(" + outputCycleIndex + ")");
        }


        return cycleToOutputIndex;
    }

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    private final BasicInputParser parser;


    public DelimitedTextFileWithHeaderIterator(final BasicInputParser parser) {
        this.parser = parser;
        if (!parser.hasNext()) {
            throw new PicardException("No header line found in file " + parser.getFileName());
        }
        final String[] columnLabels = parser.next();
        for (int i = 0; i < columnLabels.length; ++i) {
            columnLabelIndices.put(columnLabels[i], i);
        }

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    protected int doWork() {
        IOUtil.assertFileIsReadable(INPUT);
        IOUtil.assertFileIsWritable(OUTPUT);


        if (INPUT.getAbsolutePath().endsWith(".sam")) {
            throw new PicardException("SAM files are not supported");
        }


        final SAMFileHeader samFileHeader = new SAMFileReader(INPUT).getFileHeader();
        for (final String comment : COMMENT) {
            if (comment.contains("\n")) {
                throw new PicardException("Comments can not contain a new line");
            }
            samFileHeader.addComment(comment);
        }


        BamFileIoUtils.reheaderBamFile(samFileHeader, INPUT, OUTPUT, CREATE_MD5_FILE, CREATE_INDEX);

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                                                               CHART_OUTPUT.getAbsolutePath(),
                                                               INPUT.getName(),
                                                               this.plotSubtitle);


            if (rResult != 0) {
                throw new PicardException("Problem invoking R to generate plot.");
            }
        }
    }

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picard.illumina.IlluminaBasecallsToFastq

picard.illumina.IlluminaBasecallsToSam

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