Examples of PicardException

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

Examples of net.sf.picard.PicardException

    }


    private void assertPairedMates(final SAMRecord record1, final SAMRecord record2) {
        if (! (record1.getFirstOfPairFlag() && record2.getSecondOfPairFlag() ||
               record2.getFirstOfPairFlag() && record1.getSecondOfPairFlag() ) ) {
            throw new PicardException("Illegal mate state: " + record1.getReadName());
        }
    }

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Examples of picard.PicardException

        } else {
            // todo -- potential optimization is to check if contig.name == contig, as this in general will be true
            SAMSequenceRecord contigInfo = super.getSequenceDictionary().getSequence(contig);


            if (stop > contigInfo.getSequenceLength())
                throw new PicardException("Query asks for data past end of contig");


            if ( start < myCache.start || stop > myCache.stop || myCache.seq == null || myCache.seq.getContigIndex() != contigInfo.getSequenceIndex() ) {
                cacheMisses++;
                myCache.start = Math.max(start - cacheMissBackup, 0);
                myCache.stop  = Math.min(start + cacheSize + cacheMissBackup, contigInfo.getSequenceLength());

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Examples of picard.PicardException

        }


        writer.close();


        if (freader1.hasNext() || freader2.hasNext()) {
            throw new PicardException("Input paired fastq files must be the same length");
        }


        return readCount;
    }

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Examples of picard.PicardException

        final byte[] quals = StringUtil.stringToBytes(frec.getBaseQualityString());
        convertQuality(quals, QUALITY_FORMAT);
        for (final byte qual : quals) {
            final int uQual = qual & 0xff;
            if (uQual < MIN_Q || uQual > MAX_Q) {
                throw new PicardException("Base quality " + uQual + " is not in the range " + MIN_Q + ".." +
                MAX_Q + " for read " + frec.getReadHeader());
            }
        }
        srec.setBaseQualities(quals);

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Examples of picard.PicardException

        toks = getReadNameTokens(readName2, 2, freader2);
        final String baseName2 = toks[0] ;
        final String num2 = toks[1];


        if (!baseName1.equals(baseName2)) {
            throw new PicardException(String.format("In paired mode, read name 1 (%s) does not match read name 2 (%s)", baseName1,baseName2));
        }


        final boolean num1Blank = StringUtil.isBlank(num1);
        final boolean num2Blank = StringUtil.isBlank(num2);
        if (num1Blank || num2Blank) {
            if(!num1Blank) throw new PicardException(error(freader1,"Pair 1 number is missing (" +readName1+ "). Both pair numbers must be present or neither."));       //num1 != blank and num2   == blank
            else if(!num2Blank) throw new PicardException(error(freader2, "Pair 2 number is missing (" +readName2+ "). Both pair numbers must be present or neither.")); //num1 == blank and num =2 != blank 
        } else {
            if (!num1.equals("1")) throw new PicardException(error(freader1,"Pair 1 number must be 1 ("+readName1+")"));
            if (!num2.equals("2")) throw new PicardException(error(freader2,"Pair 2 number must be 2 ("+readName2+")"));
        }


        return baseName1 ;
    }

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Examples of picard.PicardException

        return baseName1 ;
    }


    /** Breaks up read name into baseName and number separated by the last / */
    private String [] getReadNameTokens(final String readName, final int pairNum, final FastqReader freader) {
        if(readName.equals("")) throw new PicardException(error(freader,"Pair read name "+pairNum+" cannot be empty: "+readName));


        final int idx = readName.lastIndexOf("/");
        final String result[] = new String[2];


        if (idx == -1) {

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Examples of picard.PicardException

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


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

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Examples of picard.PicardException

            if (!delimiter) {
                 parts[index] = new String(line,start,line.length-start);
            }
        }
        catch (ArrayIndexOutOfBoundsException e) {
            throw new PicardException("Unexpected number of elements found when parsing file " +
                    this.getFileName() + ": " + index + ".  Expected a maximum of " +
                    this.getWordCount() + " elements per line:" + new String(line,0,line.length), e);
        }
        return parts;
    }

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Examples of picard.PicardException

     * Either set this value if not already set, or if already set, throw an exception if new value != current value.
     */
    public void setOrCheckTile(final int tile) {
        if (tileIsSet()) {
            if (this.tile != tile) {
                throw new PicardException("Tile number mismatch for " + this + " : " + this.tile + " != " + tile);
            }
        } else {
            this.tile = tile;
        }
    }

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Examples of picard.PicardException

     * Either set this value if not already set, or if already set, throw an exception if new value != current value.
     */
    public void setOrCheckLane(final int lane) {
        if (laneIsSet()) {
            if (this.lane != lane) {
                throw new PicardException("Lane number mismatch for " + this + " : " + this.lane + " != " + lane);
            }
        } else {
            this.lane = lane;
        }
    }

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