diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRodWithGenomeLoc.java b/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRodWithGenomeLoc.java
index 22acf323b..bd7f96e8c 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRodWithGenomeLoc.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRodWithGenomeLoc.java
@@ -273,7 +273,7 @@ public class PlinkRodWithGenomeLoc extends BasicReferenceOrderedDatum implements
                 if ( line != null ) {
                     String[] snpInfo = line.split("\\s+");
                     PlinkVariantInfo variant = new PlinkVariantInfo(snpInfo[1],true);
-                    variant.setGenomeLoc(GenomeLocParser.parseGenomeLoc(snpInfo[0],Long.valueOf(snpInfo[2]), Long.valueOf(snpInfo[2])+1));
+                    variant.setGenomeLoc(GenomeLocParser.parseGenomeLoc(snpInfo[0],Long.valueOf(snpInfo[3]), Long.valueOf(snpInfo[3])));
                     variant.setAlleles(snpInfo[4],snpInfo[5]);
                     variants.add(variant);
                 }
@@ -337,15 +337,15 @@ public class PlinkRodWithGenomeLoc extends BasicReferenceOrderedDatum implements
 
                         if ( snpMajorMode ) {
                             sampleOffset = sampleOffset + 4;
-                            while ( sampleOffset > samples.size() -1 ) {
+                            if ( sampleOffset > samples.size() -1 ) {
                                 snpOffset ++;
-                                sampleOffset = sampleOffset % samples.size();
+                                sampleOffset = 0;
                             }
                         } else {
                             snpOffset = snpOffset + 4;
-                            while ( snpOffset > variants.size() -1 ) {
+                            if ( snpOffset > variants.size() -1 ) {
                                 sampleOffset ++;
-                                snpOffset = snpOffset % samples.size();
+                                snpOffset = 0;
                             }
                         }
 
@@ -371,22 +371,12 @@ public class PlinkRodWithGenomeLoc extends BasicReferenceOrderedDatum implements
 
             if ( major ) {
                 sampleOffset++;
-                while ( sampleOffset > sampleNames.size()-1 ) {  //using offsets for comparison; size 5 == offset 4
-                    snpOffset++;
-                    sampleOffset = sampleOffset % sampleNames.size();
-                }
-                if ( snpOffset > variants.size()-1) {
-                    // done with file; early return
+                if ( sampleOffset > sampleNames.size()-1 ) {  //using offsets for comparison; size 5 == offset 4
                     return;
                 }
             } else {
                 snpOffset++;
-                while( snpOffset > variants.size()-1 ) {
-                    sampleOffset++;
-                    snpOffset = snpOffset % variants.size();
-                }
-                if ( sampleOffset > sampleNames.size()-1 ) {
-                    // done with file; early return
+                if( snpOffset > variants.size()-1 ) {
                     return;
                 }
             }
@@ -444,11 +434,17 @@ class PlinkVariantInfo implements Comparable {
     }
 
     public void setAlleles(String al1, String al2) {
-        locAllele1 = al1;
+        if ( al1.equals("0") ) {
+            // encoding for a site at which no variants were detected
+            locAllele1 = al2;
+        } else {
+            locAllele1 = al1;
+        }
         locAllele2 = al2;
         if ( ! isSNP() ) {
             siteIndelLength = Math.max(locAllele1.length(),locAllele2.length());
         }
+
     }
 
     // CONSTRUCTOR
@@ -501,7 +497,7 @@ class PlinkVariantInfo implements Comparable {
         if ( genoTYPE == 0 ) {
             alleleStr[0] = locAllele1;
             alleleStr[1] = locAllele1;
-        } else if (genoTYPE == 1) {
+        } else if (genoTYPE == 2) {
             alleleStr[0] = locAllele1;
             alleleStr[1] = locAllele2;
         } else if (genoTYPE == 3 ) {
diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodTest.java
index 8c1bbcd32..a384e73a9 100755
--- a/java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodTest.java
@@ -161,5 +161,46 @@ public class PlinkRodTest extends BaseTest {
         } catch (FileNotFoundException e) {
             throw new StingException("Test file for testBinaryPedFileNoIndels() could not be found",e);
         }
+
+        // iterate through the ROD and get stuff
+        ArrayList<GenomeLoc> lociInRod = new ArrayList<GenomeLoc>();
+        ArrayList<ArrayList<Genotype>> genotypesInRod = new ArrayList<ArrayList<Genotype>>();
+        ArrayList<ArrayList<String>> samplesInRod = new ArrayList<ArrayList<String>>();
+
+        do {
+            lociInRod.add(rod.getLocation());
+            genotypesInRod.add(rod.getGenotypes());
+            samplesInRod.add(rod.getVariantSampleNames());
+        } while ( rod.parseLine(null,null) );
+
+        List<String> expecLoc = Arrays.asList("1:123456","1:14327877","2:22074511","3:134787","3:178678","4:829645","4:5234132","12:1268713");
+
+        for ( int i = 0; i < expecLoc.size(); i ++ ) {
+            Assert.assertEquals("That locus "+(i+1)+" in the rod is correct", expecLoc.get(i), lociInRod.get(i).toString());
+        }
+
+        List<String> expecAlleles = Arrays.asList("AA","AA","AA","GG","GG","GG","AA","TA","TT","CC","CC","GC","TC","CC","TT",
+                                                  "GG","GG","AG","TT","CC","CT","TG","GG","GG");
+        List<Boolean> expecHet = Arrays.asList(false,false,false,false,false,false,false,true,false,false,false,true,true,false,
+                    false,false,false,true,false,false,true,true,false,false);
+        List<String> expecName = Arrays.asList("NA12878","NA12890","NA07000","NA12878","NA12890","NA07000","NA12878","NA12890","NA07000",
+                    "NA12878","NA12890","NA07000","NA12878","NA12890","NA07000","NA12878","NA12890","NA07000","NA12878","NA12890","NA07000",
+                "NA12878","NA12890","NA07000");
+        int snpNo = 1;
+        int indiv = 1;
+        int alleleOffset = 0;
+        for ( ArrayList<Genotype> snp : genotypesInRod ) {
+            for ( Genotype gen : snp ) {
+                String alStr = gen.getAlleles().get(0).getBases()+gen.getAlleles().get(1).getBases();
+                Assert.assertEquals("That the allele of person "+indiv+" for snp "+snpNo+" is correct "+
+                                    "(allele offset "+alleleOffset+")", expecAlleles.get(alleleOffset),alStr);
+                Assert.assertEquals("That the genotype of person "+indiv+" for snp "+snpNo+" is properly set", expecHet.get(alleleOffset),gen.isHet());
+                Assert.assertEquals("That the name of person "+indiv+" for snp "+snpNo+" is correct", expecName.get(alleleOffset),samplesInRod.get(snpNo-1).get(indiv-1));
+                indiv++;
+                alleleOffset++;
+            }
+            indiv = 1;
+            snpNo++;
+        }
     }
 }