Splitting responsibility for AbstractWsgMetricsCollector class

LadDeep · Apr 7, 2023 · c147cbb · c147cbb
1 parent 2816540
commit c147cbb
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Showing 4 changed files with 76 additions and 31 deletions.
diff --git a/src/main/java/picard/analysis/AbstractWgsMetricsCollector.java b/src/main/java/picard/analysis/AbstractWgsMetricsCollector.java
@@ -89,6 +89,8 @@ public abstract class AbstractWgsMetricsCollector<T extends AbstractRecordAndOff
      */
     protected long counter = 0;
 
+    protected WgsHistogramCollector histogram;
+
     /**
      * Creates a collector and initializes the inner data structures
      *
@@ -106,6 +108,7 @@ public abstract class AbstractWgsMetricsCollector<T extends AbstractRecordAndOff
         this.coverageCap    = coverageCap;
         this.intervals      = intervals;
         this.usingStopAfter = collectWgsMetrics.STOP_AFTER > 0;
+        this.histogram = new WgsHistogramCollector(coverageCap);
     }
 
     /**
@@ -134,33 +137,33 @@ public void addToMetricsFile(final MetricsFile<WgsMetrics, Integer> file,
 
         // add them to the file
         file.addMetric(metrics);
-        file.addHistogram(getHighQualityDepthHistogram());
-        if (includeBQHistogram) addBaseQHistogram(file);
-    }
-
-    protected void addBaseQHistogram(final MetricsFile<WgsMetrics, Integer> file) {
-        file.addHistogram(getUnfilteredBaseQHistogram());
-    }
-
-    protected Histogram<Integer> getHighQualityDepthHistogram() {
-        return getHistogram(highQualityDepthHistogramArray, "coverage", "high_quality_coverage_count");
-    }
-
-    protected Histogram<Integer> getUnfilteredDepthHistogram() {
-        return getHistogram(unfilteredDepthHistogramArray, "coverage", "unfiltered_coverage_count");
-    }
-
-    protected Histogram<Integer> getUnfilteredBaseQHistogram() {
-        return getHistogram(unfilteredBaseQHistogramArray, "baseq", "unfiltered_baseq_count");
+        file.addHistogram(histogram.getHighQualityDepthHistogram());
+        if (includeBQHistogram) histogram.addBaseQHistogram(file);
     }
 
-    protected Histogram<Integer> getHistogram(final long[] array, final String binLabel, final String valueLabel) {
-        final Histogram<Integer> histogram = new Histogram<>(binLabel, valueLabel);
-        for (int i = 0; i < array.length; ++i) {
-            histogram.increment(i, array[i]);
-        }
-        return histogram;
-    }
+//    protected void addBaseQHistogram(final MetricsFile<WgsMetrics, Integer> file) {
+//        file.addHistogram(getUnfilteredBaseQHistogram());
+//    }
+//
+//    protected Histogram<Integer> getHighQualityDepthHistogram() {
+//        return getHistogram(highQualityDepthHistogramArray, "coverage", "high_quality_coverage_count");
+//    }
+//
+//    protected Histogram<Integer> getUnfilteredDepthHistogram() {
+//        return getHistogram(unfilteredDepthHistogramArray, "coverage", "unfiltered_coverage_count");
+//    }
+//
+//    protected Histogram<Integer> getUnfilteredBaseQHistogram() {
+//        return getHistogram(unfilteredBaseQHistogramArray, "baseq", "unfiltered_baseq_count");
+//    }
+//
+//    protected Histogram<Integer> getHistogram(final long[] array, final String binLabel, final String valueLabel) {
+//        final Histogram<Integer> histogram = new Histogram<>(binLabel, valueLabel);
+//        for (int i = 0; i < array.length; ++i) {
+//            histogram.increment(i, array[i]);
+//        }
+//        return histogram;
+//    }
 
     /**
      * Creates CollectWgsMetrics.WgsMetrics - the object holding the result of CollectWgsMetrics
@@ -176,8 +179,8 @@ protected WgsMetrics getMetrics(final CountingFilter dupeFilter,
             final CountingPairedFilter pairFilter) {
         return collectWgsMetrics.generateWgsMetrics(
                 this.intervals,
-                getHighQualityDepthHistogram(),
-                getUnfilteredDepthHistogram(),
+                histogram.getHighQualityDepthHistogram(),
+                histogram.getUnfilteredDepthHistogram(),
                 collectWgsMetrics.getBasesExcludedBy(adapterFilter),
                 collectWgsMetrics.getBasesExcludedBy(mapqFilter),
                 collectWgsMetrics.getBasesExcludedBy(dupeFilter),
@@ -186,7 +189,7 @@ protected WgsMetrics getMetrics(final CountingFilter dupeFilter,
                 basesExcludedByOverlap,
                 basesExcludedByCapping,
                 coverageCap,
-                getUnfilteredBaseQHistogram(),
+                histogram.getUnfilteredBaseQHistogram(),
                 collectWgsMetrics.SAMPLE_SIZE);
     }
 
@@ -218,4 +221,5 @@ boolean isReferenceBaseN(final int position, final ReferenceSequence ref) {
         final byte base = ref.getBases()[position - 1];
         return SequenceUtil.isNoCall(base);
     }
+
 }
diff --git a/src/main/java/picard/analysis/CollectWgsMetrics.java b/src/main/java/picard/analysis/CollectWgsMetrics.java
@@ -232,6 +232,7 @@ protected int doWork() {
         iterator.setIncludeNonPfReads(false);
 
         final AbstractWgsMetricsCollector<?> collector = getCollector(COVERAGE_CAP, getIntervalsToExamine());
+        final WgsHistogramCollector histogramCollector = new WgsHistogramCollector(COVERAGE_CAP);
         final WgsMetricsProcessor processor = getWgsMetricsProcessor(progress, refWalker, iterator, collector);
         processor.processFile();
 
@@ -243,7 +244,7 @@ protected int doWork() {
             // Write out theoretical sensitivity results.
             final MetricsFile<TheoreticalSensitivityMetrics, ?> theoreticalSensitivityMetrics = getMetricsFile();
             log.info("Calculating theoretical sentitivity at " + ALLELE_FRACTION.size() + " allele fractions.");
-            List<TheoreticalSensitivityMetrics> tsm = TheoreticalSensitivity.calculateSensitivities(SAMPLE_SIZE, collector.getUnfilteredDepthHistogram(), collector.getUnfilteredBaseQHistogram(), ALLELE_FRACTION);
+            List<TheoreticalSensitivityMetrics> tsm = TheoreticalSensitivity.calculateSensitivities(SAMPLE_SIZE, collector.histogram.getUnfilteredDepthHistogram(), histogramCollector.getUnfilteredDepthHistogram(), ALLELE_FRACTION);
             theoreticalSensitivityMetrics.addAllMetrics(tsm);
             theoreticalSensitivityMetrics.write(THEORETICAL_SENSITIVITY_OUTPUT);
         }

diff --git a/src/main/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverage.java b/src/main/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverage.java
@@ -242,12 +242,12 @@ public void addToMetricsFile(final MetricsFile<WgsMetrics, Integer> file,
             file.addHistogram(highQualityDepthHistogramNonZero);
 
             if (includeBQHistogram) {
-                addBaseQHistogram(file);
+                histogram.addBaseQHistogram(file);
             }
         }
 
         protected Histogram<Integer> getDepthHistogram() {
-            return getHistogram(highQualityDepthHistogramArray, "coverage", "count_WHOLE_GENOME");
+            return histogram.getHistogram(highQualityDepthHistogramArray, "coverage", "count_WHOLE_GENOME");
         }
 
         private Histogram<Integer> getDepthHistogramNonZero() {

diff --git a/src/main/java/picard/analysis/WgsHistogramCollector.java b/src/main/java/picard/analysis/WgsHistogramCollector.java
@@ -0,0 +1,40 @@
+package picard.analysis;
+
+import htsjdk.samtools.metrics.MetricsFile;
+import htsjdk.samtools.util.Histogram;
+
+public class WgsHistogramCollector {
+    private long[] highQualityDepthHistogramArray;
+    protected final long[] unfilteredDepthHistogramArray;
+    protected final long[] unfilteredBaseQHistogramArray;
+
+    public WgsHistogramCollector(final int coverageCap) {
+        unfilteredDepthHistogramArray = new long[coverageCap + 1];
+        highQualityDepthHistogramArray = new long[coverageCap + 1];
+        unfilteredBaseQHistogramArray = new long[Byte.MAX_VALUE];
+    }
+
+    protected void addBaseQHistogram(final MetricsFile<WgsMetrics, Integer> file) {
+        file.addHistogram(getUnfilteredBaseQHistogram());
+    }
+
+    protected Histogram<Integer> getHighQualityDepthHistogram() {
+        return getHistogram(highQualityDepthHistogramArray, "coverage", "high_quality_coverage_count");
+    }
+
+    protected Histogram<Integer> getUnfilteredDepthHistogram() {
+        return getHistogram(unfilteredDepthHistogramArray, "coverage", "unfiltered_coverage_count");
+    }
+
+    protected Histogram<Integer> getUnfilteredBaseQHistogram() {
+        return getHistogram(unfilteredBaseQHistogramArray, "baseq", "unfiltered_baseq_count");
+    }
+
+    protected Histogram<Integer> getHistogram(final long[] array, final String binLabel, final String valueLabel) {
+        final Histogram<Integer> histogram = new Histogram<>(binLabel, valueLabel);
+        for (int i = 0; i < array.length; ++i) {
+            histogram.increment(i, array[i]);
+        }
+        return histogram;
+    }
+}