diff --git a/R/plot_Annotations_BinnedTiTv.R b/R/plot_Annotations_BinnedTiTv.R
index ee74e8c55..89c5f1c69 100644
--- a/R/plot_Annotations_BinnedTiTv.R
+++ b/R/plot_Annotations_BinnedTiTv.R
@@ -15,35 +15,23 @@ c <- read.table(input, header=T)
 # Plot TiTv ratio as a function of the annotation
 #
 
-gt = c[c$numVariants>minBinCutoff & c$category==0,]
+all = c[c$numVariants>minBinCutoff & c$category==0,]
 novel = c[c$numVariants>minBinCutoff & c$category==1,]
 dbsnp = c[c$numVariants>minBinCutoff & c$category==2,]
 
 d = c[c$numVariants>minBinCutoff,]
-cmin = min(d$titv)
-cmax = max(d$titv)
+ymin = min(d$titv)
+ymax = max(d$titv)
+xmin = min(d$value)
+xmax = max(d$value)
 
 outfile = paste(outputDir, "binnedTiTv.", annotationName, ".pdf", sep="")
 pdf(outfile, height=7, width=7)
 par(cex=1.1)
-plot(gt$value,gt$titv,xlab=annotationName,ylab="Ti/Tv ratio",pch=20);
-m = weighted.mean(gt$value,gt$numVariants/sum(gt$numVariants))
-ma = gt[gt$value > m,]
-mb = gt[gt$value < m,]
-m75 = weighted.mean(ma$value,ma$numVariants/sum(ma$numVariants))
-m25 = weighted.mean(mb$value,mb$numVariants/sum(mb$numVariants))
-abline(v=m,lty=2)
-abline(v=m75,lty=2)
-abline(v=m25,lty=2)
-dev.off()
-
-outfile = paste(outputDir, "binnedTiTv_novel.", annotationName, ".pdf", sep="")
-pdf(outfile, height=7, width=7)
-par(cex=1.1)
-plot(gt$value,gt$titv,xlab=annotationName,ylab="Ti/Tv ratio",pch=20,yim=c(cmin,cmax));
-m = weighted.mean(gt$value,gt$numVariants/sum(gt$numVariants))
-ma = gt[gt$value > m,]
-mb = gt[gt$value < m,]
+plot(all$value,all$titv,xlab=annotationName,ylab="Ti/Tv ratio",pch=20,ylim=c(ymin,ymax));
+m = weighted.mean(all$value,all$numVariants/sum(all$numVariants))
+ma = all[all$value > m,]
+mb = all[all$value < m,]
 m75 = weighted.mean(ma$value,ma$numVariants/sum(ma$numVariants))
 m25 = weighted.mean(mb$value,mb$numVariants/sum(mb$numVariants))
 abline(v=m,lty=2)
@@ -51,21 +39,24 @@ abline(v=m75,lty=2)
 abline(v=m25,lty=2)
 points(novel$value,novel$titv,col="green",pch=20)
 points(dbsnp$value,dbsnp$titv,col="blue",pch=20)
-legend("topleft", c("overall","novel","dbsnp"),col=c("black","green","blue"),pch=c(20,20,20))
+legend("topleft", c("all","novel","dbsnp"),col=c("black","green","blue"),pch=c(20,20,20))
 dev.off()
 
-
-outfile = paste(outputDir, "binnedTiTv_quartiles.", annotationName, ".pdf", sep="")
+outfile = paste(outputDir, "binnedTiTv_log.", annotationName, ".pdf", sep="")
 pdf(outfile, height=7, width=7)
 par(cex=1.1)
-plot(gt$value,gt$titv,xlab=annotationName,ylab="Ti/Tv ratio",pch=20,xlim=c(0,80))
+plot(all$value,all$titv,xlab=annotationName,log="x",ylab="Ti/Tv ratio",pch=20,ylim=c(ymin,ymax));
 abline(v=m,lty=2)
 abline(v=m75,lty=2)
 abline(v=m25,lty=2)
+points(novel$value,novel$titv,col="green",pch=20)
+points(dbsnp$value,dbsnp$titv,col="blue",pch=20)
+legend("topleft", c("all","novel","dbsnp"),col=c("black","green","blue"),pch=c(20,20,20))
 dev.off()
 
+
 outfile = paste(outputDir, "binnedTiTv_hist.", annotationName, ".pdf", sep="")
 pdf(outfile, height=7, width=7)
 par(cex=1.1)
-plot(gt$value,gt$numVariants,xlab=annotationName,ylab="num Variants in bin",type="h");
+plot(all$value,all$numVariants,xlab=annotationName,ylab="num Variants in bin",type="h");
 dev.off()
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
index d8cc5593f..f404e2b30 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -56,8 +56,9 @@ public class RecalDataManager {
     public final static String COLOR_SPACE_INCONSISTENCY_TAG = "ZC"; // A new tag made up for the recalibrator which will hold an array of ints which say if this base is inconsistent with its color
     private static boolean warnUserNullReadGroup = false;
     private static boolean warnUserNoColorSpace = false;
+    private static boolean warnUserNullPlatform = false;
 
-    public static final String versionString = "v2.2.16"; // Major version, minor version, and build number
+    public static final String versionString = "v2.2.17"; // Major version, minor version, and build number
 
     RecalDataManager() {
     	data = new NestedHashMap();
@@ -242,6 +243,13 @@ public class RecalDataManager {
         }
 
         if ( readGroup.getPlatform() == null ) {
+            if( !warnUserNullPlatform ) {
+                Utils.warnUser("The input .bam file contains reads with no read group. " +
+                                    "Defaulting to platform = " + RAC.DEFAULT_PLATFORM + ". " +
+                                    "First observed at read with name = " + read.getReadName() );
+                Utils.warnUser("Users may set the default platform using the --default_platform <String> argument.");
+                warnUserNullPlatform = true;
+            }
             readGroup.setPlatform( RAC.DEFAULT_PLATFORM );            
         }
     }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
index 2ecff405b..3b4ca52e9 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
@@ -58,10 +58,17 @@ public class AnnotationDataManager {
         // Loop over each annotation in the vcf record
         final Map<String,String> infoField = variant.getInfoValues();
         for( String annotationKey : infoField.keySet() ) {
-            if( annotationKey.equalsIgnoreCase("AC") ) {
-                continue; // This annotation isn't a float value
+
+            float value = 0.0f;
+            boolean skipThisAnnotation = false;
+            try {
+                value = Float.parseFloat( infoField.get( annotationKey ) );
+            } catch( Exception e ) { // BUGBUG: Make this exception more specific. NumberFormatException??
+                skipThisAnnotation = true; // skip over annotations that aren't floats, like "AC"?? and "DB"
+            }
+            if( skipThisAnnotation ) {
+                continue; // skip over annotations that aren't floats, like "AC"?? and "DB"
             }
-            final float value = Float.parseFloat( infoField.get( annotationKey ) );
 
             if( variant.getID().equals(".") ) { // This is a novel variant
                 TreeSet<AnnotationDatum> treeSet = dataNovel.get( annotationKey );
@@ -212,7 +219,7 @@ public class AnnotationDataManager {
                 numTi += datum.numTransitions;
                 numTv += datum.numTransversions;
                 lastDatum = datum;
-                if( numTi + numTv >= MAX_VARIANTS_PER_BIN/3 ) { // This annotation bin is full
+                if( numTi + numTv >= MAX_VARIANTS_PER_BIN/2 ) { // This annotation bin is full
                     float titv;
                     if( numTv == 0) { titv = 0.0f; }
                     else { titv = ((float) numTi) / ((float) numTv); }