X_FILTERED_COUNT

 the number of reads in the locus that pass the FeatureMap filters, regardless of whether the considered base matches the reference or not

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

@@ -7,6 +7,12 @@
 
 public interface FeatureMapper {
 
+    enum FilterStatus {
+        None,
+        Filtered,
+        NoFeatureAndFiltered
+    };
+
     void        forEachOnRead(GATKRead read, ReferenceContext referenceContext, Consumer<? super FlowFeatureMapper.MappedFeature> action);
-    boolean     noFeatureButFilterAt(GATKRead read, ReferenceContext referenceContext, int start);
+    FilterStatus noFeatureButFilterAt(GATKRead read, ReferenceContext referenceContext, int start);
 }

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

@@ -161,7 +161,7 @@ protected static class MappedFeature implements Comparable<MappedFeature> {
         byte[]      readBases;
         byte[]      refBases;
         int         readBasesOffset; // offset of read bases array
-        int         start;      // location (on rerence)
+        int         start;      // location (on reference)
         int         offsetDelta;
         double      score;
         int         readCount;
@@ -405,7 +405,7 @@ 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) ) {
+                if ( mapper.noFeatureButFilterAt(rc.read, rc.referenceContext, fr.start) == FeatureMapper.FilterStatus.Filtered ) {
                     fr.filteredCount++;
                 }
             }

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

@@ -222,7 +222,7 @@ private int calcSmq(final byte[] quals, int from, int to, boolean median) {
         }
     }
 
-    public boolean noFeatureButFilterAt(GATKRead read, ReferenceContext referenceContext, int start) {
+    public FilterStatus noFeatureButFilterAt(GATKRead read, ReferenceContext referenceContext, int start) {
 
         // access bases
         final byte[]      bases = read.getBasesNoCopy();
@@ -245,7 +245,7 @@ public boolean noFeatureButFilterAt(GATKRead read, ReferenceContext referenceCon
                 // break out if not enough clearing
                 if ( (start < referenceContext.getStart() + refOfs + identBefore) ||
                         (start >= referenceContext.getStart() + refOfs + length - identAfter) )
-                    return false;
+                    return FilterStatus.Filtered;
 
                 int         delta = start - (referenceContext.getStart() + refOfs);
                 readOfs += delta;
@@ -269,10 +269,10 @@ public boolean noFeatureButFilterAt(GATKRead read, ReferenceContext referenceCon
                         continue;
                     }
 
-                    // this is it! no feature but filtred in
-                    return true;
+                    // this is it! no feature but filtered in
+                    return FilterStatus.NoFeatureAndFiltered;
                 } else
-                    return false;
+                    return FilterStatus.Filtered;
 
             } else {
 
@@ -287,7 +287,7 @@ public boolean noFeatureButFilterAt(GATKRead read, ReferenceContext referenceCon
         };
 
         // if here, false
-        return false;
+        return FilterStatus.None;
     }
 
 }

src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java

@@ -591,11 +591,11 @@ public void applyBaseClipping(final int clipLeftBase, final int clipRightBase, b
 
     private void applyClipping(int clipLeft, final int leftHmerClip, int clipRight, final int rightHmerClip, final boolean spread){
         if ((clipLeft < 0) || (clipRight < 0)  || (clipLeft >= getKeyLength() ) || ( clipRight >= getKeyLength())) {
-            throw new IllegalStateException("Weird read clip calculated");
+            throw new IllegalStateException(String.format("Weird read clip calculated: left/right/keyLength %d/%d/%d", clipLeft, clipRight, getKeyLength()));
         }
 
-        if ((leftHmerClip < 0) || (rightHmerClip < 0)  || (leftHmerClip >= 14 ) || ( rightHmerClip >= 14)) {
-            throw new IllegalStateException("Weird read clip calculated");
+        if ((leftHmerClip < 0) || (rightHmerClip < 0)  || (leftHmerClip >= (getMaxHmer() + 2) ) || ( rightHmerClip >= (getMaxHmer() + 2))) {
+            throw new IllegalStateException(String.format("Weird read clip calculated: left/right/maxHmer+2 %d/%d/%d", leftHmerClip, rightHmerClip, getMaxHmer() + 2));
         }
 
         final int originalLength = key.length;