import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
/**
 * Calculate the beta-hats that best fit case read counts given the panel of normals.
 *
 * @param normalsPseudoinverse the log-normalized or reduced-panel pseudoinverse from a panel of normals
 * @param input a {@code TxS} matrix where {@code T} is the number of targets and {@code S} the number of count groups (e.g. case samples).
 * @return never {@code null} an {@code NxS} matrix, where N is the number of samples in
 *  the panel and S the original name of count groups.
 */
@VisibleForTesting
public static RealMatrix calculateBetaHats(final RealMatrix normalsPseudoinverse,
                                           final RealMatrix input,
                                           final double epsilon) {
    Utils.nonNull(normalsPseudoinverse, "Normals inverse matrix cannot be null.");
    Utils.nonNull(input, "Input counts cannot be null.");
    Utils.validateArg(epsilon > 0, String.format("Invalid epsilon value, must be > 0: %f", epsilon));
    final double targetThreshold = (Math.log(epsilon) / Math.log(2)) + 1;

    // copy case samples in order to mask targets in-place and mask (set to zero) targets with coverage below threshold
    final RealMatrix maskedInput = input.copy();
    maskedInput.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(final int row, final int column, final double value) {
            return value > targetThreshold ? value : 0;
        }
    });

    return normalsPseudoinverse.multiply(maskedInput);
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
/**
 * Final pre-panel normalization that consists of dividing all counts by the median of
 * its column and log it with base 2.
 * <p>
 *     The normalization occurs in-place.
 * </p>
 *
 * @param readCounts the input counts to normalize.
 */
@VisibleForTesting
static void normalizeAndLogReadCounts(final ReadCountCollection readCounts, final Logger logger) {
    final RealMatrix counts = readCounts.counts();
    final Median medianCalculator = new Median();

    final double[] medians = IntStream.range(0, counts.getColumnDimension()).mapToDouble(col -> medianCalculator.evaluate(counts.getColumn(col))).toArray();
    counts.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(final int row, final int column, final double value) {
            return Math.log(Math.max(EPSILON, value / medians[column])) * INV_LN_2;
        }
    });

    logger.info("Counts normalized by the column median and log2'd.");
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
/**
 * Calculates the median of column medians and subtract it from all counts.
 * @param readCounts the input counts to center.
 * @return the median of medians that has been subtracted from all counts.
 */
@VisibleForTesting
static double subtractMedianOfMedians(final ReadCountCollection readCounts, final Logger logger) {
    final RealMatrix counts = readCounts.counts();
    final Median medianCalculator = new Median();
    final double[] columnMedians = MatrixSummaryUtils.getColumnMedians(counts);

    final double medianOfMedians = medianCalculator.evaluate(columnMedians);
    counts.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(final int row, final int column, final double value) {
            return value - medianOfMedians;
        }
    });
    logger.info(String.format("Counts centered around the median of medians %.2f", medianOfMedians));
    return medianOfMedians;
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
public static Pair<ReadCountCollection, double[]> simulatedData(final int numTargets, final int numSamples) {
    final List<Target> phonyTargets = SimulatedTargets.phonyTargets(numTargets);
    final List<String> phonySamples = SimulatedSamples.phonySamples(numSamples);

    final Random random = new Random(13);
    final double[] gcContentByTarget = IntStream.range(0, numTargets)
            .mapToDouble(n -> 0.5 + 0.2*random.nextGaussian())
            .map(x -> Math.min(x,0.95)).map(x -> Math.max(x,0.05)).toArray();
    final double[] gcBiasByTarget = Arrays.stream(gcContentByTarget).map(QUADRATIC_GC_BIAS_CURVE::apply).toArray();

    // model mainly GC bias with a small random amount of non-GC bias
    // thus noise after GC correction should be nearly zero
    final RealMatrix counts = new Array2DRowRealMatrix(numTargets, numSamples);
    counts.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(final int target, final int column, final double value) {
            return gcBiasByTarget[target]*(1.0 + 0.01*random.nextDouble());
        }
    });
    final ReadCountCollection rcc = new ReadCountCollection(phonyTargets, phonySamples, counts);
    return new ImmutablePair<>(rcc, gcContentByTarget);
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
private static Pair<RealMatrix, double[]> simulateData(final int numSamples,
                                                       final int numIntervals) {
    final Random random = new Random(RANDOM_SEED);
    final double[] intervalGCContent = IntStream.range(0, numIntervals)
            .mapToDouble(n -> 0.5 + 0.2 * random.nextGaussian())
            .map(x -> Math.min(x, 0.95)).map(x -> Math.max(x, 0.05))
            .toArray();
    final double[] intervalGCBias = Arrays.stream(intervalGCContent)
            .map(QUADRATIC_GC_BIAS_CURVE::apply)
            .toArray();

    //model GC bias along with a small random amount of uniform non-GC-bias noise;
    //remaining noise after GC-bias correction should be only arise from the latter
    final RealMatrix readCounts = new Array2DRowRealMatrix(numSamples, numIntervals);
    readCounts.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(final int sample, final int interval, final double value) {
            return (int) (MEAN_READ_DEPTH * intervalGCBias[interval] * (1. + NON_GC_BIAS_NOISE_LEVEL * random.nextDouble()));
        }
    });
    return new ImmutablePair<>(readCounts, intervalGCContent);
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
@Override
  public ClassifierResult apply(Matrix data) {	
  if ( VERB>0 ) System.out.println("ERSP apply");
  // Do the standard pre-processing
  data = preproc(data);
  
  // Linearly classifying the data
  if( VERB>1 ) System.out.println(TAG+ "Classifying with linear classifier");
  Matrix fraw = applyLinearClassifier(data, 0);
  if( VERB>1 ) System.out.println(TAG+ "Results from the classifier (fraw): " + fraw.toString());
  Matrix f = new Matrix(fraw.copy());
  Matrix p = new Matrix(f.copy());
  p.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
			 public double visit(int row, int column, double value) {
              return 1. / (1. + Math.exp(-value));
			 }
		});
  if ( VERB>1 ) System.out.println(TAG+ "Results from the classifier (p): " + p.toString());
  return new ClassifierResult(f, fraw, p, data);
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
public ClassifierResult apply(Matrix data){
  if ( VERB>1 ) System.out.println(TAG+ " preproc");
  // Do the standard pre-processing
  data = preproc(data);
  
  // Linearly classifying the data
  if ( VERB>1 ) System.out.println(TAG+  "Classifying with linear classifier");
  Matrix fraw = applyLinearClassifier(data, 0);
  if ( VERB>1 ) System.out.println(TAG+  "Results from the classifier (fraw): " + fraw.toString());
  Matrix f = new Matrix(fraw.copy());
  Matrix p = new Matrix(f.copy());
  // map to probabilities using the logistic operator
  p.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
			 public double visit(int row, int column, double value) {
              return 1. / (1. + Math.exp(-value));
			 }
		});
  if ( VERB>=0 ) System.out.println(TAG+  "Results from the classifier (p): " + p.toString());
  return new ClassifierResult(f, fraw, p, data);		  
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
private RealMatrix createMatrixOfGaussianValues(int numRows, int numCols, final double mean, final double sigma) {
    final RealMatrix bigCounts = new Array2DRowRealMatrix(numRows, numCols);
    final RandomDataGenerator randomDataGenerator = new RandomDataGenerator();
    randomDataGenerator.reSeed(337337337);
    bigCounts.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(int row, int column, double value) {
            return randomDataGenerator.nextGaussian(mean, sigma);
        }
    });
    return bigCounts;
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
@Test
public void testPerfectFit() {
    double[] betaHat = regression.estimateRegressionParameters();
    TestUtils.assertEquals(betaHat,
                           new double[]{ 11.0, 1.0 / 2.0, 2.0 / 3.0, 3.0 / 4.0, 4.0 / 5.0, 5.0 / 6.0 },
                           1e-14);
    double[] residuals = regression.estimateResiduals();
    TestUtils.assertEquals(residuals, new double[]{0d,0d,0d,0d,0d,0d},
                           1e-14);
    RealMatrix errors =
        new Array2DRowRealMatrix(regression.estimateRegressionParametersVariance(), false);
    final double[] s = { 1.0, -1.0 /  2.0, -1.0 /  3.0, -1.0 /  4.0, -1.0 /  5.0, -1.0 /  6.0 };
    RealMatrix referenceVariance = new Array2DRowRealMatrix(s.length, s.length);
    referenceVariance.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(int row, int column, double value) {
            if (row == 0) {
                return s[column];
            }
            double x = s[row] * s[column];
            return (row == column) ? 2 * x : x;
        }
    });
   Assert.assertEquals(0.0,
                 errors.subtract(referenceVariance).getNorm(),
                 5.0e-16 * referenceVariance.getNorm());
   Assert.assertEquals(1, ((OLSMultipleLinearRegression) regression).calculateRSquared(), 1E-12);
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
/**
 * Impute zero counts to the median of non-zero values in the enclosing target row.
 *
 * <p>The imputation is done in-place, thus the input matrix is well be modified as a result of this call.</p>
 *
 * @param readCounts the input and output read-count matrix.
 */
public static void imputeZeroCountsAsTargetMedians(final ReadCountCollection readCounts, final Logger logger) {

    final RealMatrix counts = readCounts.counts();
    final int targetCount = counts.getRowDimension();

    final Median medianCalculator = new Median();
    int totalCounts = counts.getColumnDimension() * counts.getRowDimension();

    // Get the number of zeroes contained in the counts.
    final long totalZeroCounts = IntStream.range(0, targetCount)
            .mapToLong(t -> DoubleStream.of(counts.getRow(t))
                    .filter(c -> c == 0.0).count()).sum();

    // Get the median of each row, not including any entries that are zero.
    final double[] medians = IntStream.range(0, targetCount)
            .mapToDouble(t -> medianCalculator.evaluate(
                    DoubleStream.of(counts.getRow(t))
                            .filter(c -> c != 0.0)
                            .toArray()
            )).toArray();

    // Change any zeros in the counts to the median for the row.
    counts.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(final int row, final int column, final double value) {
            return value != 0 ? value : medians[row];
        }
    });

    if (totalZeroCounts > 0) {
        final double totalZeroCountsPercentage = 100.0 * (totalZeroCounts / totalCounts);
        logger.info(String.format("Some 0.0 counts (%d out of %d, %.2f%%) were imputed to their enclosing target " +
                "non-zero median", totalZeroCounts, totalZeroCounts, totalZeroCountsPercentage));
    } else {
        logger.info("No count is 0.0 thus no count needed to be imputed.");
    }
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
/**
 * Standardize read counts (per-target).
 * Note: modification is done in-place.
 *
 * @param counts original read counts
 */
private void standardizeByTarget(final RealMatrix counts) {
    final double[] rowMeans = GATKProtectedMathUtils.rowMeans(counts);
    final double[] rowStdDev = GATKProtectedMathUtils.rowStdDevs(counts);

    counts.walkInColumnOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(final int row, final int column, final double value) {
            return (value - rowMeans[row]) / rowStdDev[row];
        }

    });
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
/**
 * Standardize read counts (per-sample).
 * Note: modification is done in-place.
 *
 * @param counts original read counts
 */
private void standardizeBySample(final RealMatrix counts) {
    final double[] columnMeans = GATKProtectedMathUtils.columnMeans(counts);
    final double[] columnStdDev = GATKProtectedMathUtils.columnStdDevs(counts);

    counts.walkInColumnOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(int row, int column, double value) {
            return (value - columnMeans[column]) / columnStdDev[column];
        }

    });
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
public static RealMatrix getAsRealMatrix(final LikelihoodMatrix<Allele> matrix) {
    final RealMatrix result = new Array2DRowRealMatrix(matrix.numberOfAlleles(), matrix.numberOfReads());
    result.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(int row, int column, double value) {
            return matrix.get(row, column);
        }
    });
    return result;
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
/**
 * Target-factor normalizes a {@link RealMatrix} in-place given target factors..
 */
static void factorNormalize(final RealMatrix input, final double[] targetFactors) {
    Utils.nonNull(input, "Input matrix cannot be null.");
    Utils.nonNull(targetFactors, "Target factors cannot be null.");
    Utils.validateArg(targetFactors.length == input.getRowDimension(),
            "Number of target factors does not correspond to the number of rows.");
    // Divide all counts by the target factor for the row.
    input.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(final int row, final int column, final double value) {
            return value / targetFactors[row];
        }
    });
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
/**
 * SVD and Pseudo inverse calculation.
 *
 * @param logNormalized the input counts for the SVD and reduction steps, fully normalized and already logged.
 * @param requestedNumberOfEigensamples user requested number of eigensamples for the reduced panel.
 * @return never {@code null}.
 */
@VisibleForTesting
static ReductionResult calculateReducedPanelAndPInverses(final ReadCountCollection logNormalized,
                                                         final OptionalInt requestedNumberOfEigensamples,
                                                         final Logger logger,
                                                         final JavaSparkContext ctx) {

    if (ctx == null) {
        logger.warn("No Spark context provided, not going to use Spark...");
    }

    final RealMatrix logNormalizedCounts = logNormalized.counts();
    final int numberOfCountColumns = logNormalizedCounts.getColumnDimension();

    logger.info("Starting the SVD decomposition of the log-normalized counts ...");
    final long svdStartTime = System.currentTimeMillis();
    final SVD logNormalizedSVD = SVDFactory.createSVD(logNormalized.counts(), ctx);
    final long svdEndTime = System.currentTimeMillis();
    logger.info(String.format("Finished the SVD decomposition of the log-normal counts. Elapse of %d seconds", (svdEndTime - svdStartTime) / 1000));

    final int numberOfEigensamples = determineNumberOfEigensamples(requestedNumberOfEigensamples, numberOfCountColumns, logNormalizedSVD, logger);
    logger.info(String.format("Including %d eigensamples in the reduced PoN", numberOfEigensamples));

    final double[] singularValues = logNormalizedSVD.getSingularValues();
    final RealMatrix reducedCounts = logNormalizedSVD.getU().getSubMatrix(0, logNormalizedCounts.getRowDimension()-1, 0, numberOfEigensamples - 1).copy();
    reducedCounts.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(final int row, final int column, final double value) { return singularValues[column]*value; }
    });

    // The Pseudo inverse comes nearly for free from having run the SVD decomposition.
    final RealMatrix logNormalizedPseudoInverse = logNormalizedSVD.getPinv();

    logger.info("Calculating the reduced PoN inverse matrix...");
    final long riStartTime = System.currentTimeMillis();
    final RealMatrix reducedCountsPseudoInverse = SVDFactory.createSVD(reducedCounts, ctx).getPinv();
    final long riEndTime = System.currentTimeMillis();
    logger.info(String.format("Finished calculating the reduced PoN inverse matrix. Elapse of %d seconds", (riEndTime - riStartTime) / 1000));
    return new ReductionResult(logNormalizedPseudoInverse, reducedCounts, reducedCountsPseudoInverse, logNormalizedSVD.getSingularValues());
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
/**
 * Preprocess (i.e., transform to fractional coverage, correct GC bias, filter, impute, and truncate) 
 * and standardize read counts from a panel of normals.
 * All inputs are assumed to be valid.
 * The dimensions of {@code readCounts} should be samples x intervals.
 * To reduce memory footprint, {@code readCounts} is modified in place when possible.
 * Filtering is performed by using boolean arrays to keep track of intervals and samples
 * that have been filtered at any step and masking {@code readCounts} with them appropriately.
 * If {@code intervalGCContent} is null, GC-bias correction will not be performed.
 */
static PreprocessedStandardizedResult preprocessAndStandardizePanel(final RealMatrix readCounts,
                                                                    final double[] intervalGCContent,
                                                                    final double minimumIntervalMedianPercentile,
                                                                    final double maximumZerosInSamplePercentage,
                                                                    final double maximumZerosInIntervalPercentage,
                                                                    final double extremeSampleMedianPercentile,
                                                                    final boolean doImputeZeros,
                                                                    final double extremeOutlierTruncationPercentile) {
    //preprocess (transform to fractional coverage, correct GC bias, filter, impute, truncate) and return copy of submatrix
    logger.info("Preprocessing read counts...");
    final PreprocessedStandardizedResult preprocessedStandardizedResult = preprocessPanel(readCounts, intervalGCContent,
            minimumIntervalMedianPercentile, maximumZerosInSamplePercentage, maximumZerosInIntervalPercentage,
            extremeSampleMedianPercentile, doImputeZeros, extremeOutlierTruncationPercentile);
    logger.info("Panel read counts preprocessed.");

    //standardize in place
    logger.info("Standardizing read counts...");
    divideBySampleMedianAndTransformToLog2(preprocessedStandardizedResult.preprocessedStandardizedValues);
    logger.info("Subtracting median of sample medians...");
    final double[] sampleLog2Medians = MatrixSummaryUtils.getRowMedians(preprocessedStandardizedResult.preprocessedStandardizedValues);
    final double medianOfSampleMedians = new Median().evaluate(sampleLog2Medians);
    preprocessedStandardizedResult.preprocessedStandardizedValues
            .walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(int sampleIndex, int intervalIndex, double value) {
            return value - medianOfSampleMedians;
        }
    });
    logger.info("Panel read counts standardized.");

    return preprocessedStandardizedResult;
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
/**
 * Preprocess (i.e., transform to fractional coverage and correct GC bias)
 * and standardize read counts for samples when no panel of normals is available.
 * The original {@code readCounts} has dimensions 1 x intervals and is not modified.
 * If {@code intervalGCContent} is null, GC-bias correction will not be performed
 */
public static RealMatrix preprocessAndStandardizeSample(final double[] readCounts,
                                                        final double[] intervalGCContent) {
    Utils.nonNull(readCounts);
    Utils.validateArg(intervalGCContent == null || readCounts.length == intervalGCContent.length,
            "Number of intervals for read counts must match those for GC-content annotations.");

    RealMatrix result = new Array2DRowRealMatrix(new double[][]{readCounts});

    //preprocess (transform to fractional coverage, correct GC bias) copy in place
    logger.info("Preprocessing read counts...");
    transformToFractionalCoverage(result);
    performOptionalGCBiasCorrection(result, intervalGCContent);
    logger.info("Sample read counts preprocessed.");

    //standardize copy in place
    logger.info("Standardizing read counts...");
    divideBySampleMedianAndTransformToLog2(result);
    logger.info("Subtracting sample median...");
    final double[] sampleLog2Medians = MatrixSummaryUtils.getRowMedians(result);
    result.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(int sampleIndex, int intervalIndex, double value) {
            return value - sampleLog2Medians[sampleIndex];
        }
    });
    logger.info("Sample read counts standardized.");

    return result;
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
private static void transformToFractionalCoverage(final RealMatrix matrix) {
    logger.info("Transforming read counts to fractional coverage...");
    final double[] sampleSums = MathUtils.rowSums(matrix);
    matrix.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(int sampleIndex, int intervalIndex, double value) {
            return value / sampleSums[sampleIndex];
        }
    });
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
private static void divideBySampleMedianAndTransformToLog2(final RealMatrix matrix) {
    logger.info("Dividing by sample medians and transforming to log2 space...");
    final double[] sampleMedians = MatrixSummaryUtils.getRowMedians(matrix);
    matrix.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(int sampleIndex, int intervalIndex, double value) {
            return safeLog2(value / sampleMedians[sampleIndex]);
        }
    });
}
 

import org.apache.commons.math3.linear.DefaultRealMatrixChangingVisitor; //导入依赖的package包/类
private static RealMatrix createMatrixOfGaussianValues(final int numRows,
                                                       final int numColumns,
                                                       final double mean,
                                                       final double sigma) {
    final RealMatrix largeMatrix = new Array2DRowRealMatrix(numRows, numColumns);
    final RandomDataGenerator randomDataGenerator = new RandomDataGenerator();
    randomDataGenerator.reSeed(337337337);
    largeMatrix.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
        @Override
        public double visit(int row, int column, double value) {
            return randomDataGenerator.nextGaussian(mean, sigma);
        }
    });
    return largeMatrix;
}