diff --git a/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelArgumentCollection.java index 27cb55189..fdcccfa2d 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelArgumentCollection.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelArgumentCollection.java @@ -998,10 +998,7 @@ public boolean includeARDInLogLikelihood() { /** * Validate parameters. * - * TODO github/gatk-protected issue #843 -- more validations - * positive/negative values - * Maxes greater than mins - * + * TODO github/gatk-protected issue #1058 */ public void validate() { diff --git a/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelCopyRatioEmissionProbabilityCalculator.java b/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelCopyRatioEmissionProbabilityCalculator.java index fbdadc3ae..5b1beb7af 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelCopyRatioEmissionProbabilityCalculator.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelCopyRatioEmissionProbabilityCalculator.java @@ -234,7 +234,7 @@ static double getLogProbabilityLaplaceApproximationNormalizationConstant(final d } /** - * TODO github/gatk-protected issue #855 -- rewrite using org.broadinstitute.hellbender.utils.Utils.stream + * TODO github/gatk-protected issue #853 -- rewrite using org.broadinstitute.hellbender.utils.Utils.stream */ private static double[] loadDoubleArrayTable(final InputStream inputStream) { final Scanner reader = new Scanner(inputStream); @@ -246,7 +246,7 @@ private static double[] loadDoubleArrayTable(final InputStream inputStream) { } /** - * TODO github/gatk-protected issue #855 -- rewrite using org.broadinstitute.hellbender.utils.Utils.stream + * TODO github/gatk-protected issue #853 -- rewrite using org.broadinstitute.hellbender.utils.Utils.stream */ private static double[][] loadDouble2DArrayTable(final InputStream inputStream) { final Scanner reader = new Scanner(inputStream); diff --git a/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelEMComputeBlock.java b/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelEMComputeBlock.java index 9d9b3cd7c..00d055e6e 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelEMComputeBlock.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelEMComputeBlock.java @@ -32,8 +32,7 @@ * This class represents an immutable block of data containers, query methods and cloners corresponding to * a partition of the target space. * - * TODO github/gatk-protected issue #853 -- logging in spark mode (log4j is not serializable) - * TODO github/gatk-protected issue #853 -- use instrumentation to measure memory consumption + * TODO github/gatk-protected issue #1059 * * @implNote Methods that manipulate INDArrays must make sure to leave queried values from * {@link CoverageModelEMComputeBlock#icg} unchanged. For example, to calculate the A.B.C + D, diff --git a/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelEMWorkspace.java b/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelEMWorkspace.java index c3123b2db..2994b6f30 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelEMWorkspace.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelEMWorkspace.java @@ -493,6 +493,7 @@ private static ReadCountCollection getTargetSortedReadCountCollection(@Nonnull f } /** + * TODO github/gatk-protected issue #1055 -- consider adding more filters * Process read counts and filter targets and/or samples as follows: * *
@@ -502,11 +503,6 @@ private static ReadCountCollection getTargetSortedReadCountCollection(@Nonnull f * * @implNote it is best to keep this filter static and functional in design for robustness/clarity. * - * TODO github/gatk-protected issue #855 -- consider adding more filters - * - remove targets with very high and very low GC content (can be done externally) - * - remove targets with lots of repeats (can be done externally) - * - in the learning mode, remove a target if too many are masked across the samples (in that case, max likelihood - * parameter estimation is unreliable) */ private static ReadCountCollection processReadCountCollection(@Nonnull final ReadCountCollection rawReadCounts, @Nonnull final CoverageModelArgumentCollection args, @@ -622,7 +618,7 @@ private void pushInitialDataToComputeBlocks() { .map(idx -> isMaskedForLearning(rawReadCountBlock[idx], germlinePloidyBlock[idx], config.getMinLearningReadCount()) ? 0 : 1) .toArray(); - /* TODO github/gatk-protected issue #855 -- in the future, this must be replaced with a sample- + /* TODO github/gatk-protected issue #748 -- in the future, this must be replaced with a sample- * and target-specific value calculated from the mapping quality distribution of each target */ final double[] mappingErrorRateBlock = IntStream.range(0, rawReadCountBlock.length) .mapToDouble(idx -> config.getMappingErrorRate()) @@ -2629,7 +2625,7 @@ protected void writeBiasCovariatesARDHistory(final String outputPath) { /** * Saves copy-ratio-related posteriors to disk. * - * TODO github/gatk-protected issue #855 -- write local copy ratio posteriors as well + * TODO github/gatk-protected issue #1056 -- write local copy ratio posteriors as well? * * @param outputPath the output path */ diff --git a/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelGlobalConstants.java b/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelGlobalConstants.java index fa40a7be4..964ea8ddb 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelGlobalConstants.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelGlobalConstants.java @@ -53,8 +53,6 @@ public final class CoverageModelGlobalConstants implements Serializable { public static final double RANDOM_UNEXPLAINED_VARIANCE_MAX = 0.0; /** - * TODO -- either estimate this from data for expose to user - * * Gaussian random standard deviation for bias covariates */ public static final double RANDOM_BIAS_COVARIATES_STD = 0.1; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/cachemanager/ImmutableComputableGraph.java b/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/cachemanager/ImmutableComputableGraph.java index ec7287753..789e4f2b4 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/cachemanager/ImmutableComputableGraph.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/coveragemodel/cachemanager/ImmutableComputableGraph.java @@ -102,8 +102,6 @@ * Otherwise, only the cache status will go out of date. Unchanged nodes are passed as reference to the new instance. * JVM's garbage collector will free up the memory for old cached nodes in sequential computations. * - * TODO github/gatk-protected issue # 999 --- Improve ImmutableComputableGraph - * * @author Mehrtash Babadi <mehrtash@broadinstitute.org> */ public final class ImmutableComputableGraph implements Serializable { diff --git a/src/main/java/org/broadinstitute/hellbender/tools/exome/germlinehmm/IntegerCopyNumberState.java b/src/main/java/org/broadinstitute/hellbender/tools/exome/germlinehmm/IntegerCopyNumberState.java index efa8abcdd..1189519c1 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/exome/germlinehmm/IntegerCopyNumberState.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/exome/germlinehmm/IntegerCopyNumberState.java @@ -49,12 +49,12 @@ public Allele toAllele() { } /** - * TODO github/gatk-protected issue #855 -- this is required for VCF creation + * TODO github/gatk-protected issue #1057 -- this is required for VCF creation * @param header an instance of {@link VCFHeader} */ @Override public void addHeaderLineTo(@Nonnull VCFHeader header) { - throw new UnsupportedOperationException("github/gatk-protected issue #855"); + throw new UnsupportedOperationException("github/gatk-protected issue #1057"); } @Override diff --git a/src/main/java/org/broadinstitute/hellbender/utils/hmm/segmentation/HMMSegmentProcessor.java b/src/main/java/org/broadinstitute/hellbender/utils/hmm/segmentation/HMMSegmentProcessor.java index bc8695468..be3031580 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/hmm/segmentation/HMMSegmentProcessor.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/hmm/segmentation/HMMSegmentProcessor.java @@ -28,8 +28,10 @@ import java.util.stream.IntStream; /** - * TODO github/gatk-protected issue #855 -- this is a last-minute fork of {@link HMMPostProcessor}. - * It just does segmentation (no VCF creation) + * This class generates constant copy number segments from Viterbi states, calculates segment summary + * statistics from forward-backward results, and write the output as .seg files. + * + * TODO github/gatk-protected issue #1056 -- Viterbi vs. local posteriors * * @author Mehrtash Babadi <mehrtash@broadinstitute.org> */