Several improvements to AssessNA12878 and KB

-- Bugfix for BAMs containing reads without real (M,I,D,N) operators.  Simply needed to set validation stringency to SILENT in the read. Added a BadCigar filter to the SAMRecord stream anyway
-- Add capture all sites mode to AssessNA12878: will write all sites to the badSites VCF, regardless of whether they are bad.  It's useful if you essentially want to annotate a VCF with KB information for later analysis, such as computing ROC curves
-- Add ignore filters mode to AssessNA12878: will as expected treat all sites in the input VCF calls as PASS, even if the site has a FILTER field setting
-- Add minPNonRef argument to AssessNA12878: this will consider a site not called even if the NA12878 genotype is not 0/0 if the PLs are present and the PL for 0/0 isn't greater than this value.  It allows us to easily differentiate low confidence non-ref sites obtained via multi-sample calling from highly confident non-ref calls that might be real TP or FPs

public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java

@@ -29,7 +29,8 @@ import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import net.sf.samtools.CigarOperator;
 import net.sf.samtools.SAMFileReader;
-import net.sf.samtools.SAMRecordIterator;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.util.CloseableIterator;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -154,7 +155,7 @@ public final class LocusIteratorByState extends LocusIterator {
      * @param reader a non-null reader
      * @param it an iterator from reader that has the reads we want to use to create ReadBackPileups
      */
-    public LocusIteratorByState(final SAMFileReader reader, final SAMRecordIterator it) {
+    public LocusIteratorByState(final SAMFileReader reader, final CloseableIterator<SAMRecord> it) {
         this(new GATKSAMIterator(it),
                 new LIBSDownsamplingInfo(false, 0),
                 true,