FlowFeatureMapper: X_FILTERED_COUNT semantics adjusted and documented more accurately

src/main/java/org/broadinstitute/hellbender/tools/walkers/featuremapping/FlowFeatureMapper.java

@@ -337,7 +337,7 @@ public VCFHeader makeVCFHeader(final SAMSequenceDictionary sequenceDictionary, f
         headerInfo.add(new VCFInfoHeaderLine(VCF_MAPQ, 1, VCFHeaderLineType.Integer, "Read mapqe"));
         headerInfo.add(new VCFInfoHeaderLine(VCF_CIGAR, 1, VCFHeaderLineType.String, "Read CIGAR"));
         headerInfo.add(new VCFInfoHeaderLine(VCF_READ_COUNT, 1, VCFHeaderLineType.Integer, "Number of reads containing this location"));
-        headerInfo.add(new VCFInfoHeaderLine(VCF_FILTERED_COUNT, 1, VCFHeaderLineType.Integer, "Number of reads containing this location that agree with reference according to fitler"));
+        headerInfo.add(new VCFInfoHeaderLine(VCF_FILTERED_COUNT, 1, VCFHeaderLineType.Integer, "Number of reads containing this location that pass the adjacent base filter"));
         headerInfo.add(new VCFInfoHeaderLine(VCF_FC1, 1, VCFHeaderLineType.Integer, "Number of M bases different on read from references"));
         headerInfo.add(new VCFInfoHeaderLine(VCF_FC2, 1, VCFHeaderLineType.Integer, "Number of features before score threshold filter"));
         headerInfo.add(new VCFInfoHeaderLine(VCF_LENGTH, 1, VCFHeaderLineType.Integer, "Read length"));
@@ -475,7 +475,8 @@ private void enrichFeature(final MappedFeature fr) {
         for ( ReadContext rc : readQueue ) {
             if ( rc.read.contains(loc) ) {
                 fr.readCount++;
-                if ( mapper.noFeatureButFilterAt(rc.read, rc.referenceContext, fr.start) == FeatureMapper.FilterStatus.Filtered ) {
+                FeatureMapper.FilterStatus fs = mapper.noFeatureButFilterAt(rc.read, rc.referenceContext, fr.start);
+                if ( (fs == FeatureMapper.FilterStatus.Filtered) || (fs == FeatureMapper.FilterStatus.NoFeatureAndFiltered) ) {
                     fr.filteredCount++;
                 }
             }

src/main/java/org/broadinstitute/hellbender/tools/walkers/featuremapping/SNVMapper.java

@@ -277,40 +277,37 @@ public FilterStatus noFeatureButFilterAt(GATKRead read, ReferenceContext referen
                 readOfs += delta;
                 refOfs += delta;
 
-                if ( bases[readOfs] == ref[refOfs] ) {
-
-                    // check that this is really a SNV (must be surrounded by identical ref)
-                    boolean     surrounded = true;
-                    for ( int i = 0 ; i < surroundBefore && surrounded ; i++ ) {
-                        final int bIndex = readOfs-1-i;
-                        final int rIndex = refOfs-1-i;
-                        if ( bIndex < 0 || bIndex >= bases.length || rIndex < 0 || rIndex >= ref.length ) {
-                            surrounded = false;
-                            continue;
-                        }
-                        if ( bases[bIndex] != ref[rIndex] ) {
-                            surrounded = false;
-                        }
+                final boolean noFeature = bases[readOfs] == ref[refOfs];
+
+                // check that this is really a SNV (must be surrounded by identical ref)
+                boolean     surrounded = true;
+                for ( int i = 0 ; i < surroundBefore && surrounded ; i++ ) {
+                    final int bIndex = readOfs-1-i;
+                    final int rIndex = refOfs-1-i;
+                    if ( bIndex < 0 || bIndex >= bases.length || rIndex < 0 || rIndex >= ref.length ) {
+                        surrounded = false;
+                        continue;
                     }
-                    for (int i = 0; i < surroundAfter && surrounded ; i++ ) {
-                        final int bIndex = readOfs+1+i;
-                        final int rIndex = refOfs+1+i;
-                        if ( bIndex < 0 || bIndex >= bases.length || rIndex < 0 || rIndex >= ref.length ) {
-                            surrounded = false;
-                            continue;
-                        }
-                        if ( bases[bIndex] != ref[rIndex] ) {
-                            surrounded = false;
-                        }
+                    if ( bases[bIndex] != ref[rIndex] ) {
+                        surrounded = false;
                     }
-                    if ( !surrounded ) {
+                }
+                for (int i = 0; i < surroundAfter && surrounded ; i++ ) {
+                    final int bIndex = readOfs+1+i;
+                    final int rIndex = refOfs+1+i;
+                    if ( bIndex < 0 || bIndex >= bases.length || rIndex < 0 || rIndex >= ref.length ) {
+                        surrounded = false;
                         continue;
                     }
+                    if ( bases[bIndex] != ref[rIndex] ) {
+                        surrounded = false;
+                    }
+                }
+                if ( !surrounded ) {
+                    continue;
+                }
 
-                    // this is it! no feature but filtered in
-                    return FilterStatus.NoFeatureAndFiltered;
-                } else
-                    return FilterStatus.Filtered;
+                return noFeature ? FilterStatus.NoFeatureAndFiltered : FilterStatus.Filtered;
 
             } else {