Examples of org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException

Package org.broadinstitute.gatk.utils.exceptions

Examples of org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException
A trivial extension around GATKException to mark exceptions that have been reviewed for correctness, completeness, etc. By using this exception you are saying "this is the right error message". GATKException is now just a catch all for lazy users.

        } else if ( loc.compareContigs(firstLoc) == 0 ) {
            write(wWriter,String.format("%n"));
            write(wWriter,String.format("%d\t%s",loc.getStart(),dataPoint.toString()));
        } else {
            // todo -- maybe allow this to open a new file for the new chromosome?
            throw new ReviewedGATKException("Attempting to write multiple contigs into wiggle file, first contig was "+firstLoc.getContig()+" most recent "+loc.getContig());
        }
    }

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    // NOTE -- THIS CODE IS SYNCHRONIZED WITH CODE IN THE SAMTOOLS REPOSITORY.  CHANGES TO THIS CODE SHOULD BE
    // NOTE -- PUSHED BACK TO HENG LI
    //
    // ####################################################################################################
    public int hmm_glocal(final byte[] ref, final byte[] query, int qstart, int l_query, final byte[] _iqual, int[] state, byte[] q) {
        if ( ref == null ) throw new ReviewedGATKException("BUG: ref sequence is null");
        if ( query == null ) throw new ReviewedGATKException("BUG: query sequence is null");
        if ( _iqual == null ) throw new ReviewedGATKException("BUG: query quality vector is null");
        if ( query.length != _iqual.length ) throw new ReviewedGATKException("BUG: read sequence length != qual length");
        if ( l_query < 1 ) throw new ReviewedGATKException("BUG: length of query sequence < 0: " + l_query);
        if ( qstart < 0 ) throw new ReviewedGATKException("BUG: query sequence start < 0: " + qstart);


        //if ( q != null && q.length != state.length ) throw new ReviewedGATKException("BUG: BAQ quality length != read sequence length");
        //if ( state != null && state.length != l_query ) throw new ReviewedGATKException("BUG: state length != read sequence length");


    int i, k;

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            final int bq = (int)read.getBaseQualities()[i] + 64;
            final int baq_i = (int)baq[i];
            final int tag = bq - baq_i;
            // problem with the calculation of the correction factor; this is our problem
            if ( tag < 0 )
                throw new ReviewedGATKException("BAQ tag calculation error.  BAQ value above base quality at " + read);
            // the original quality is too high, almost certainly due to using the wrong encoding in the BAM file
            if ( tag > Byte.MAX_VALUE )
                throw new UserException.MisencodedBAM(read, "we encountered an extremely high quality score (" + (int)read.getBaseQualities()[i] + ") with BAQ correction factor of " + baq_i);
            bqTag[i] = (byte)tag;
        }

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//    final SimpleTimer total = new SimpleTimer();
//    final SimpleTimer local = new SimpleTimer();
//    int n = 0;
    public BAQCalculationResult calcBAQFromHMM(byte[] ref, byte[] query, byte[] quals, int queryStart, int queryEnd ) {
//        total.restart();
        if ( queryStart < 0 ) throw new ReviewedGATKException("BUG: queryStart < 0: " + queryStart);
        if ( queryEnd < 0 ) throw new ReviewedGATKException("BUG: queryEnd < 0: " + queryEnd);
        if ( queryEnd < queryStart ) throw new ReviewedGATKException("BUG: queryStart < queryEnd : " + queryStart + " end =" + queryEnd);


        // note -- assumes ref is offset from the *CLIPPED* start
        BAQCalculationResult baqResult = new BAQCalculationResult(query, quals, ref);
        int queryLen = queryEnd - queryStart;
//        local.restart();

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                        queryStop = readI;
                    }
                    // in the else case we aren't including soft clipped bases, so we don't update
                    // queryStart or queryStop
                    break;
                default: throw new ReviewedGATKException("BUG: Unexpected CIGAR element " + elt + " in read " + read.getReadName());
            }
        }


        if ( queryStop == queryStart ) {
            // this read is completely clipped away, and yet is present in the file for some reason

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                        baqResult.bq[i] = capBaseByBAQ( baqResult.rawQuals[i], baqResult.bq[i], baqResult.state[i], expectedPos );
                    }
                    readI += l; refI += l;
                    break;
                default:
                    throw new ReviewedGATKException("BUG: Unexpected CIGAR element " + elt + " in read " + read.getReadName());
            }
        }
        if ( readI != read.getReadLength() ) // odd cigar string
            System.arraycopy(baqResult.rawQuals, 0, baqResult.bq, 0, baqResult.bq.length);

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                if ( hmmResult != null ) {
                    switch ( qmode ) {
                        case ADD_TAG:         addBAQTag(read, hmmResult.bq); break;
                        case OVERWRITE_QUALS: System.arraycopy(hmmResult.bq, 0, read.getBaseQualities(), 0, hmmResult.bq.length); break;
                        case DONT_MODIFY:     BAQQuals = hmmResult.bq; break;
                        default:              throw new ReviewedGATKException("BUG: unexpected qmode " + qmode);
                    }
                } else if ( readHasBAQTag ) {
                    // remove the BAQ tag if it's there because we cannot trust it
                    read.setAttribute(BAQ_TAG, null);
                }

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                    break;
                case Standard:
                    outputStream = standardStream;
                    break;
                default:
                    throw new ReviewedGATKException("Unexpected stream location: " + location);
            }
            this.outputStreams.put(location, outputStream);
        }
    }

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        try {
            field.setAccessible(true);
            field.set(instance, value);
        }
        catch( IllegalAccessException ex ) {
            throw new ReviewedGATKException(String.format("Could not set %s in instance %s to %s",field.getName(),instance.getClass().getName(),value.toString()));
        }
    }

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        try {
            field.setAccessible(true);
            return field.get(instance);
        }
        catch( IllegalAccessException ex ) {
            throw new ReviewedGATKException(String.format("Could not retrieve %s in instance %s",field.getName(),instance.getClass().getName()));
        }
    }

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