Package org.broadinstitute.gatk.utils.exceptions

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

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        // Target instance into which to inject the value.
        Collection<Object> targets = findTargets( source, instance );

        // Abort if no home is found for the object.
        if( targets.size() == 0 )
            throw new ReviewedGATKException("Internal command-line parser error: unable to find a home for argument matches " + argumentMatches);

        for( Object target: targets ) {
            Object value;
            boolean usedTypeDefault = false;
            if ( argumentMatches.size() != 0 ) {
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    /** Number of exons in this transcript */
    public int getNumExons() { return exons.size(); }

    /** Genomic location of the n-th exon; throws an exception if n is out of bounds */
    public GenomeLoc getExonLocation(int n) {
        if ( n >= exons.size() || n < 0 ) throw new ReviewedGATKException("Index out-of-bounds. Transcript has " + exons.size() +" exons; requested: "+n);
        return exons.get(n);
    }
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            return ((double) num)/denom;
        } else {
            if ( num == 0 && denom == 0) {
                return 0.0;
            } else {
                throw new ReviewedGATKException(String.format("The denominator of a ratio cannot be zero or less than zero: %d/%d",num,denom));
            }
        }
    }
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            return ((double) num)/denom;
        } else {
            if ( num == 0L && denom == 0L ) {
                return 0.0;
            } else {
                throw new ReviewedGATKException(String.format("The denominator of a ratio cannot be zero or less than zero: %d/%d",num,denom));
            }
        }
    }
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     * @param y vector 2
     * @return a double representing log (dotProd(10.^x,10.^y)
     */
    public static double logDotProduct(final double [] x, final double[] y) {
        if (x.length != y.length)
            throw new ReviewedGATKException("BUG: Vectors of different lengths");

        double tmpVec[] = new double[x.length];

        for (int k=0; k < tmpVec.length; k++ ) {
            tmpVec[k] = x[k]+y[k];
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     * @param y                 Second vector
     * @return Vector of same length as x and y so that z[k] = x[k]+y[k]
     */
    public static double[] vectorSum(final double[]x, final double[] y) {
        if (x.length != y.length)
            throw new ReviewedGATKException("BUG: Lengths of x and y must be the same");

        double[] result = new double[x.length];
        for (int k=0; k <x.length; k++)
            result[k] = x[k]+y[k];

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     * @param y                 Second vector
     * @return Vector of same length as x and y so that z[k] = x[k]-y[k]
     */
    public static int[] vectorDiff(final int[]x, final int[] y) {
        if (x.length != y.length)
            throw new ReviewedGATKException("BUG: Lengths of x and y must be the same");

        int[] result = new int[x.length];
        for (int k=0; k <x.length; k++)
            result[k] = x[k]-y[k];

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         * @param n operand
         * @return log10(n)
         */
        public static double get(final int n) {
            if (n < 0)
                throw new ReviewedGATKException(String.format("Can't take the log of a negative number: %d", n));
            if (n >= cache.length)
                ensureCacheContains(Math.max(n+10, 2*cache.length));
            /*
               Array lookups are not atomic.  It's possible that the reference to cache could be
               changed between the time the reference is loaded and the data is fetched from the correct
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     * @param emailAddress The user's email address, which we will store in the key and sign
     * @param signingAlgorithm The combination of hash and encryption algorithms to use to sign the key
     */
    public GATKKey ( PrivateKey privateKey, PublicKey publicKey, String emailAddress, String signingAlgorithm ) {
        if ( privateKey == null || publicKey == null || emailAddress == null || emailAddress.length() == 0 || signingAlgorithm == null ) {
            throw new ReviewedGATKException("Cannot construct GATKKey using null/empty arguments");
        }

        this.privateKey = privateKey;
        this.publicKey = publicKey;
        this.emailAddress = emailAddress;
        this.signingAlgorithm = signingAlgorithm;

        validateEmailAddress();
        generateSignature();

        if ( ! isValid() ) {
            throw new ReviewedGATKException("Newly-generated GATK key fails validation -- this should never happen!");
        }
    }
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     * @param keyFile File containing the GATK key to load
     * @param signingAlgorithm The combination of hash and encryption algorithms used to sign the key
     */
    public GATKKey ( PublicKey publicKey, File keyFile, String signingAlgorithm ) {
        if ( publicKey == null || keyFile == null || signingAlgorithm == null ) {
            throw new ReviewedGATKException("Cannot construct GATKKey using null arguments");
        }

        this.publicKey = publicKey;
        this.signingAlgorithm = signingAlgorithm;

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Related Classes of org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException

  • org.broadinstitute.gatk.engine.alignment.bwa.BWTFiles
  • org.broadinstitute.gatk.engine.alignment.bwa.java.AlignmentMatchSequence
  • org.broadinstitute.gatk.engine.alignment.reference.bwt.BWTReader
  • org.broadinstitute.gatk.engine.alignment.reference.bwt.BWTWriter
  • org.broadinstitute.gatk.engine.alignment.reference.bwt.SuffixArray
  • org.broadinstitute.gatk.engine.alignment.reference.bwt.SuffixArrayReader
  • org.broadinstitute.gatk.engine.alignment.reference.bwt.SuffixArrayWriter
  • org.broadinstitute.gatk.engine.alignment.reference.packing.PackUtils
  • org.broadinstitute.gatk.engine.contexts.AlignmentContext
  • org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils
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