Updated github issue numbers on gCNV TODO comments

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() {
 

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);

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,

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:
      *
      * <dl>
@@ -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
      */

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;

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 <[email protected]>
  */
 public final class ImmutableComputableGraph implements Serializable {

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

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 <[email protected]>
  */