From 724270b4b5e83c77545122adbac836425203e379 Mon Sep 17 00:00:00 2001
From: tedsharpe <tsharpe@broadinstitute.org>
Date: Thu, 18 Apr 2019 14:58:13 -0400
Subject: [PATCH] improve readCounts report to make categories mutually
 exclusive and tallyable

---
 .../tools/AnalyzeSaturationMutagenesis.java        | 13 ++++++-------
 .../AnalyzeSaturationMutagenesisUnitTest.java      | 14 ++++++--------
 2 files changed, 12 insertions(+), 15 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/AnalyzeSaturationMutagenesis.java b/src/main/java/org/broadinstitute/hellbender/tools/AnalyzeSaturationMutagenesis.java
index 82db4efae46..96000882d7d 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/AnalyzeSaturationMutagenesis.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/AnalyzeSaturationMutagenesis.java
@@ -35,8 +35,8 @@
  *
  * <h3>Input</h3>
  * <ul>
- * <li>A BAM file. Any combination of paired or unpaired reads can be presented.  In paired mode, the default mode
- * of operation of the program where overlapping pairs are combined bedore variant calling, the BAM must be
+ * <li>A BAM file. Any combination of paired or unpaired reads can be presented.  In paired mode (the default mode
+ * of operation of the program where overlapping pairs are combined before variant calling), the BAM must be
  * in unsorted or query-name sorted order (so that read pairs are adjacent).  The BAM file should be
  * aligned to the amplicon under scrutiny.  You may also specify a text file listing several BAMs.</li>
  * <li>A fasta-formatted reference file with the wild-type sequence of the gene as a single contig.  It's best
@@ -169,7 +169,6 @@ public void onTraversalStart() {
 
     @Override
     public void traverse() {
-        final byte[] refSeq = reference.getRefSeq();
 
         // ignore non-primary alignments
         final Stream<GATKRead> reads = getTransformedReadStream(ReadFilterLibrary.PRIMARY_LINE);
@@ -534,7 +533,7 @@ private static void writeMoleculeCounts( final MoleculeCounts moleculeCounts,
                                              final BufferedWriter writer )
             throws IOException {
         final long nInconsistentPairs = moleculeCounts.getNInconsistentPairs();
-        final long nInsufficientFlankMolecules = moleculeCounts.getnInsufficientFlank();
+        final long nInsufficientFlankMolecules = moleculeCounts.getNInsufficientFlank();
         final long nWildTypeMolecules = moleculeCounts.getNWildType();
         final long nLowQualityVariantMolecules = moleculeCounts.getNLowQualityVariant();
         final long nCalledVariantMolecules = moleculeCounts.getCalledVariant();
@@ -686,7 +685,7 @@ private int updateCoverage( final List<Interval> refCoverageList ) {
         public void bumpInconsistentPairs() { nInconsistentPairs += 1; }
         public long getNInconsistentPairs() { return nInconsistentPairs; }
         public void bumpInsufficientFlank() { nInsufficientFlank += 1; }
-        public long getnInsufficientFlank() { return nInsufficientFlank; }
+        public long getNInsufficientFlank() { return nInsufficientFlank; }
         public void bumpNLowQualityVariant() { nLowQualityVariant += 1; }
         public long getNLowQualityVariant() { return nLowQualityVariant; }
         public void bumpCalledVariant() { nCalledVariant += 1; }
@@ -1567,7 +1566,7 @@ private static List<SNV> combineVariations( final ReadReport report1, final Read
             return ReadReport.NULL_REPORT;
         }
 
-        final Interval trim = calculateTrim(read.getBaseQualitiesNoCopy(), readCounts);
+        final Interval trim = calculateTrim(read.getBaseQualitiesNoCopy());
         if ( trim.size() == 0 ) {
             readCounts.bumpNLowQualityReads();
             return ReadReport.NULL_REPORT;
@@ -1582,7 +1581,7 @@ private static List<SNV> combineVariations( final ReadReport report1, final Read
         return readReport;
     }
 
-    @VisibleForTesting static Interval calculateTrim( final byte[] quals, final ReadCounts readCounts ) {
+    @VisibleForTesting static Interval calculateTrim( final byte[] quals ) {
         // find initial end-trim
         int readStart = 0;
         int hiQCount = 0;
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/AnalyzeSaturationMutagenesisUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/AnalyzeSaturationMutagenesisUnitTest.java
index 9dfbf035831..4b68b3014e7 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/AnalyzeSaturationMutagenesisUnitTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/AnalyzeSaturationMutagenesisUnitTest.java
@@ -3,7 +3,6 @@
 import htsjdk.samtools.SAMFileHeader;
 import org.broadinstitute.hellbender.GATKBaseTest;
 import org.broadinstitute.hellbender.tools.AnalyzeSaturationMutagenesis.*;
-import org.broadinstitute.hellbender.tools.spark.utils.HopscotchMap;
 import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils;
 import org.broadinstitute.hellbender.utils.read.GATKRead;
 import org.testng.Assert;
@@ -517,23 +516,22 @@ public void testPairedApplication() {
     public void testCalculateTrim() {
         final byte BAD_Q = (byte)(minQ - 1);
         final byte GOOD_Q = (byte)minQ;
-        final ReadCounts readCounts = new ReadCounts();
         final byte[] quals = new byte[100];
         Arrays.fill(quals, BAD_Q);
-        Assert.assertEquals(calculateTrim(quals, readCounts).size(), 0);
+        Assert.assertEquals(calculateTrim(quals).size(), 0);
         Arrays.fill(quals, GOOD_Q);
-        Assert.assertEquals(calculateTrim(quals, readCounts), new Interval(0, 100));
+        Assert.assertEquals(calculateTrim(quals), new Interval(0, 100));
         quals[minLength] = BAD_Q;
-        Assert.assertEquals(calculateTrim(quals, readCounts), new Interval(0, 100));
+        Assert.assertEquals(calculateTrim(quals), new Interval(0, 100));
         quals[minLength - 1] = BAD_Q;
-        Assert.assertEquals(calculateTrim(quals, readCounts), new Interval(minLength + 1, 100));
+        Assert.assertEquals(calculateTrim(quals), new Interval(minLength + 1, 100));
         quals[quals.length - minLength] = BAD_Q;
-        Assert.assertEquals(calculateTrim(quals, readCounts), new Interval(minLength + 1, quals.length - minLength));
+        Assert.assertEquals(calculateTrim(quals), new Interval(minLength + 1, quals.length - minLength));
         Arrays.fill(quals, GOOD_Q);
         for ( int idx = minLength - 1; idx < quals.length; idx += minLength ) {
             quals[idx] = BAD_Q;
         }
-        Assert.assertEquals(calculateTrim(quals, readCounts).size(), 0);
+        Assert.assertEquals(calculateTrim(quals).size(), 0);
     }
 
     @Test