Bug fix to GenotypeConcordance. AC metrics get instantiated based on number of eval samples; if Comp has more samples, we can see AC indeces outside the bounds of the array.

Bug fix to LiftoverVariants - no barfing at reference sites.

AlleleFrequencyComparison - local changes added to make sure parsing works properly

Added HammingDistance annotation. Mostly useless. But only mostly.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4622 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java

@@ -261,13 +261,16 @@ public class GenotypeConcordance extends VariantEvaluator implements StandardEva
             qualityScoreHistograms = new QualityScoreHistograms();
         }
 
+        if ( alleleCountStats == null && eval != null && validation != null ) {
+            alleleCountStats = new ACStats(eval,validation,Genotype.Type.values().length);
+            alleleCountSummary = new ACSummaryStats(eval, validation);
+        }
+
         if (sampleStats == null) {
             if (eval != null) {
                 // initialize the concordance table
                 sampleStats = new SampleStats(eval,Genotype.Type.values().length);
-                alleleCountStats = new ACStats(eval,Genotype.Type.values().length, new CompACNames(veWalker.getLogger()));
                 sampleSummaryStats = new SampleSummaryStats(eval);
-                alleleCountSummary = new ACSummaryStats(eval, new CompACNames(veWalker.getLogger()));
                 for (final VariantContext vc : missedValidationData) {
                     determineStats(null, vc);
                 }
@@ -319,10 +322,8 @@ public class GenotypeConcordance extends VariantEvaluator implements StandardEva
                 }
 
                 sampleStats.incrValue(sample, truth, called);
-                if ( evalAC != null ) {
+                if ( evalAC != null && validationAC != null) {
                     alleleCountStats.incrValue(evalAC,truth,called);
-                }
-                if ( validationAC != null ) {
                     alleleCountStats.incrValue(validationAC,truth,called);
                 }
             }
@@ -510,24 +511,21 @@ class SampleStats implements TableType {
  * Sample stats, but for AC
  */
 class ACStats extends SampleStats {
-    private final CompACNames myComp;
     private String[] rowKeys;
 
-    public ACStats(VariantContext vc, int nGenotypeTypes, CompACNames comp) {
+    public ACStats(VariantContext evalvc, VariantContext compvc, int nGenotypeTypes) {
         super(nGenotypeTypes);
-        rowKeys = new String[2+4*vc.getGenotypes().size()];
+        rowKeys = new String[1+2*evalvc.getGenotypes().size()+1+2*compvc.getGenotypes().size()];
-        for ( int i = 0; i <= 2*vc.getGenotypes().size(); i++ ) { // todo -- assuming ploidy 2 here...
+        for ( int i = 0; i <= 2*evalvc.getGenotypes().size(); i++ ) { // todo -- assuming ploidy 2 here...
             concordanceStats.put(String.format("evalAC%d",i),new long[nGenotypeTypes][nGenotypeTypes]);
             rowKeys[i] = String.format("evalAC%d",i);
 
         }
 
-        for ( int i = 0; i <= 2*vc.getGenotypes().size(); i++ ) {
+        for ( int i = 0; i <= 2*compvc.getGenotypes().size(); i++ ) {
             concordanceStats.put(String.format("compAC%d",i), new long[nGenotypeTypes][nGenotypeTypes]);
-            rowKeys[1+2*vc.getGenotypes().size()+i] = String.format("compAC%d",i);
+            rowKeys[1+2*evalvc.getGenotypes().size()+i] = String.format("compAC%d",i);
         }
-
-        myComp = comp;
     }
 
     public String getName() {
@@ -717,23 +715,21 @@ class SampleSummaryStats implements TableType {
  * SampleSummaryStats .. but for allele counts
  */
 class ACSummaryStats extends SampleSummaryStats {
-    final private CompACNames myComp;
     private String[] rowKeys;
 
-    public ACSummaryStats (final VariantContext vc, CompACNames comp) {
+    public ACSummaryStats (final VariantContext evalvc, final VariantContext compvc) {
         concordanceSummary.put(ALL_SAMPLES_KEY, new double[COLUMN_KEYS.length]);
-        rowKeys = new String[3+4*vc.getGenotypes().size()];
+        rowKeys = new String[3+2*evalvc.getGenotypes().size() + 2*compvc.getGenotypes().size()];
         rowKeys[0] = ALL_SAMPLES_KEY;
-        for( int i = 0; i <= 2*vc.getGenotypes().size() ; i ++ ) {
+        for( int i = 0; i <= 2*evalvc.getGenotypes().size() ; i ++ ) {
             concordanceSummary.put(String.format("evalAC%d",i), new double[COLUMN_KEYS.length]);
             rowKeys[i+1] = String.format("evalAC%d",i);
         }
-        for( int i = 0; i <= 2*vc.getGenotypes().size() ; i ++ ) {
+        for( int i = 0; i <= 2*compvc.getGenotypes().size() ; i ++ ) {
             concordanceSummary.put(String.format("compAC%d",i), new double[COLUMN_KEYS.length]);
-            rowKeys[2+2*vc.getGenotypes().size()+i] = String.format("compAC%d",i);
+            rowKeys[2+2*evalvc.getGenotypes().size()+i] = String.format("compAC%d",i);
         }
 
-        myComp = comp;
     }
 
     public String getName() {

java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java

@@ -99,7 +99,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
             vc = VariantContextUtils.modifyLocation(vc, GenomeLocParser.createPotentiallyInvalidGenomeLoc(toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length));
             VariantContext newVC = VariantContext.createVariantContextWithPaddedAlleles(vc, ref.getBase(), false);
 
-            if ( VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(newVC) ) {
+            if ( originalVC.isVariant() && VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(newVC) ) {
                 logger.warn(String.format("VCF at %s / %d => %s / %d is switching substitution type %s/%s to %s/%s",
                         originalVC.getChr(), originalVC.getStart(), newVC.getChr(), newVC.getStart(),
                         originalVC.getReference(), originalVC.getAlternateAllele(0), newVC.getReference(), newVC.getAlternateAllele(0)));

java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/HammingDistance.java

@@ -0,0 +1,111 @@
+package org.broadinstitute.sting.oneoffprojects.walkers.annotator;
+
+import org.broad.tribble.util.variantcontext.Genotype;
+import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broad.tribble.vcf.VCFHeaderLineType;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+
+import java.util.*;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: chartl
+ * Date: Oct 20, 2010
+ * Time: 3:08:06 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class HammingDistance implements ExperimentalAnnotation, InfoFieldAnnotation {
+
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
+        if ( tracker == null ) {
+            return null;
+        }
+        VariantContext hamCon = tracker.getVariantContext(ref,"hamming",null,ref.getLocus(),true);
+        if ( hamCon == null ) {
+            return null;
+        }
+
+        Set<String> interSamples =  new HashSet<String>(vc.getSampleNames());
+        interSamples.retainAll(hamCon.getSampleNames());
+
+        int dist  = 0;
+        int nrd_num = 0;
+        int hamCalls = 0;
+        int vcCallsAtHamCalls = 0;
+        int num_variant = 0;
+
+        for ( String s : interSamples ) {
+            dist += dist(vc.getGenotype(s),hamCon.getGenotype(s),true);
+            nrd_num += dist(vc.getGenotype(s),hamCon.getGenotype(s),false);
+            if ( vc.getGenotype(s).isHet() || vc.getGenotype(s).isHomVar() || hamCon.getGenotype(s).isHet() || hamCon.getGenotype(s).isHomVar() ) {
+                num_variant ++;
+            }
+            if ( hamCon.getGenotype(s).isCalled() ) {
+                hamCalls++;
+                if ( vc.getGenotype(s).isCalled() ) {
+                    vcCallsAtHamCalls++;
+                }
+            }
+
+        }
+
+        HashMap<String,Object> map = new HashMap<String,Object>(1);
+        map.put("HMD",dist);
+        map.put("HCR",(0.0+vcCallsAtHamCalls)/(0.0+hamCalls));
+        map.put("NRD",(0.0+nrd_num)/(0.0+num_variant));
+        map.put("OGC",(0.0+nrd_num)/(0.0+interSamples.size()));
+        return map;
+        
+    }
+
+    public int dist(Genotype a, Genotype b, boolean weightByAC) {
+        if ( a.isNoCall() || b.isNoCall() ) {
+            return 0;
+        }
+        if ( weightByAC ) {
+            if ( a.isHomRef() ) {
+                if ( b.isHomVar() ) {
+                    return 2;
+                } else if ( b.isHet() ) {
+                    return 1;
+                } else {
+                    return 0;
+                }
+            } else if ( a.isHet() ) {
+                if ( b.isHom() ) {
+                    return 1;
+                } else {
+                    return 0;
+                }
+            } else {
+                if ( b.isHomRef() ) {
+                    return 2;
+                } else if ( b.isHet() ) {
+                    return 1;
+                } else {
+                    return 0;
+                }
+            }
+        } else {
+            if ( ! a.equals(b) ) {
+                return 1;
+            } else {
+                return 0;
+            }
+        }
+    }
+
+    public List<String> getKeyNames() { return Arrays.asList("HMD","HCR","NRD","OGC"); }
+
+    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("HMD",1, VCFHeaderLineType.Integer,"The hamming distance between record in Hamming ROD and this record"),
+            new VCFInfoHeaderLine("HCR",1,VCFHeaderLineType.Float,"The differential call rate between record in Hamming ROD and this record"),
+            new VCFInfoHeaderLine("NRD",1,VCFHeaderLineType.Float,"The Non-reference discrepancy between Hamming ROD and this record"),
+            new VCFInfoHeaderLine("OGC",1,VCFHeaderLineType.Float,"The Overall Genotype Concordance between Hamming ROD and this one")); }
+
+
+}

java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AlleleFrequencyComparison.java

@@ -12,6 +12,7 @@ import org.broadinstitute.sting.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.utils.report.utils.TableType;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -43,14 +44,21 @@ public class AlleleFrequencyComparison extends VariantEvaluator {
         if ( ! (isValidVC(eval) && isValidVC(comp))  ) {
             return null;
         } else {
-            if ( missingField(eval) ) {
+            // todo -- this is a godawful hack. The "right way" isn't working, so do it the unsafe way for now. Note that
+            // todo -- this precludes getting the AC/AF values from the info field because some may not be there...
+            /*if ( missingField(eval) ) {
                 recalculateCounts(eval);
             }
             if ( missingField(comp) ) {
                 recalculateCounts(comp);
-            }
+            }*/
-            afTable.update(getAF(eval),getAF(comp));
+            HashMap<String,Object> evalCounts = new HashMap<String,Object>(2);
-            acTable.update(getAC(eval),getAC(comp));
+            HashMap<String,Object> compCounts = new HashMap<String,Object>(2);
+
+            VariantContextUtils.calculateChromosomeCounts(eval,evalCounts,false);
+            VariantContextUtils.calculateChromosomeCounts(comp,compCounts,false);
+            afTable.update(((List<Double>)evalCounts.get("AF")).get(0),((List<Double>)compCounts.get("AF")).get(0));
+            acTable.update(((List<Integer>)evalCounts.get("AC")).get(0),((List<Integer>)compCounts.get("AC")).get(0));
         }
 
         return null; // there is nothing interesting
@@ -60,10 +68,14 @@ public class AlleleFrequencyComparison extends VariantEvaluator {
         return ! ( vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) && vc.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) );
     }
 
-    private static void recalculateCounts(VariantContext vc) {
+    private void recalculateCounts(VariantContext vc) {
-        Map<String,Object> attributes = vc.getAttributes();
+        Map<String,Object> attributes = new HashMap<String,Object>();
         VariantContextUtils.calculateChromosomeCounts(vc,attributes,false);
-        VariantContext.modifyAttributes(vc,attributes);
+        vc = VariantContext.modifyAttributes(vc,attributes);
+        getVEWalker().getLogger().debug(String.format("%s %s | %s %s",attributes.get("AC"),attributes.get("AF"),vc.getAttribute("AC"),vc.getAttribute("AF")));
+        if ( attributes.size() == 2 && missingField(vc) ) {
+            throw new org.broadinstitute.sting.utils.exceptions.StingException("VariantContext should have had attributes modified but did not");
+        }
     }
 
     private static boolean isValidVC(final VariantContext vc) {
@@ -72,7 +84,11 @@ public class AlleleFrequencyComparison extends VariantEvaluator {
 
     private static double getAF(VariantContext vc) {
         Object af = vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY);
-        if ( List.class.isAssignableFrom(af.getClass())) {
+        if ( af == null ) {
+	    //throw new UserException("Variant context "+vc.getName()+" does not have allele frequency entry which is required for this walker");
+            // still none after being re-computed; this is 0.00
+            return 0.00;
+        } else if ( List.class.isAssignableFrom(af.getClass())) {
             return ( (List<Double>) af ).get(0);
         } else if ( String.class.isAssignableFrom(af.getClass())) {
             // two possibilities
@@ -84,7 +100,7 @@ public class AlleleFrequencyComparison extends VariantEvaluator {
                     return Double.parseDouble(s);
                 }
             } catch (NumberFormatException e) {
-                throw new UserException("Allele frequency field may be improperly formatted, found AF="+s);
+                throw new UserException("Allele frequency field may be improperly formatted, found AF="+s,e);
             }
         } else if ( Double.class.isAssignableFrom(vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY).getClass())) {
             return (Double) af;
@@ -94,8 +110,11 @@ public class AlleleFrequencyComparison extends VariantEvaluator {
     }
 
     private static int getAC(VariantContext vc) {
-        Object ac = vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY);
+        Object ac = vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY);
-        if ( List.class.isAssignableFrom(ac.getClass())) {
+        if ( ac == null ) {
+            // still none after being re computed; this is 0
+            return 0;
+        } else if ( List.class.isAssignableFrom(ac.getClass())) {
             return ( (List<Integer>) ac ).get(0);
         } else if ( String.class.isAssignableFrom(ac.getClass())) {
             // two possibilities
@@ -107,9 +126,9 @@ public class AlleleFrequencyComparison extends VariantEvaluator {
                     return Integer.parseInt(s);
                 }
             } catch (NumberFormatException e) {
-                throw new UserException("Allele count field may be improperly formatted, found AC="+s);
+                throw new UserException(String.format("Allele count field may be improperly formatted, found AC=%s for record %s:%d",ac,vc.getChr(),vc.getStart()),e);
             }
-        } else if ( Double.class.isAssignableFrom(vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY).getClass())) {
+        } else if ( Integer.class.isAssignableFrom(ac.getClass())) {
             return (Integer) ac;
         } else {
             throw new UserException(String.format("Class of Allele Frequency does not appear to be formated, had AF=%s, of class %s",ac.toString(),ac.getClass()));

java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/FixRefBases.java

@@ -3,10 +3,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers.vcftools;
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFConstants;
+import org.broad.tribble.vcf.*;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFHeaderLine;
-import org.broad.tribble.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
@@ -21,6 +18,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.exceptions.*;
 
 import java.util.*;
 
@@ -46,7 +44,8 @@ public class FixRefBases extends RodWalker<Integer,Integer> {
         Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList("variant"));
 	Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
         Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), logger);
-        headerLines.add(new VCFHeaderLine("source", "SelectVariants"));
+        headerLines.add(new VCFHeaderLine("source", "FixRefBases"));
+        headerLines.add(new VCFInfoHeaderLine("FRI",1,VCFHeaderLineType.String,"The Fix-Ref-Info (if present, either \"Flipped\" or \"Fixed\")"));
         out.writeHeader(new VCFHeader(headerLines,vcfSamples));
     }
 
@@ -56,7 +55,13 @@ public class FixRefBases extends RodWalker<Integer,Integer> {
 
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         if ( tracker != null && tracker.hasROD("variant") ) {
-            VariantContext vc = tracker.getVariantContext(ref,"variant",null,context.getLocation(),true);
+            VariantContext vc = null;
+	    try {
+		vc = tracker.getVariantContext(ref,"variant",null,context.getLocation(),true);
+	    } catch ( ReviewedStingException e ) {
+		logger.warn("Multiple variants found, catching exception ",e);
+		return 0;
+	    }
             VariantContext newContext = null;
             if ( vc.isSNP() && ref.getBase() != vc.getReference().getBases()[0] && vc.getReference().length() == 1 ) {
                 if ( basesAreFlipped(vc,ref) ) {
@@ -66,13 +71,19 @@ public class FixRefBases extends RodWalker<Integer,Integer> {
                     HashSet<Allele> newAlleles = new HashSet<Allele>(vc.getAlternateAlleles());
                     Allele refAllele = Allele.create(ref.getBase(),true);
                     newAlleles.add(refAllele);
+                    HashMap<String,Object> newAttributes = new HashMap<String,Object>(vc.getAttributes());
+                    newAttributes.put("FRI",String.format("Fixed%s-%s",vc.getReference().toString(),refAllele));
                     newContext = new VariantContext("FixRefBasesVC", ref.getLocus().getContig(),
                             ref.getLocus().getStart(), ref.getLocus().getStop(), newAlleles, fixGenotypes(vc.getGenotypes(),refAllele),
                             vc.hasNegLog10PError() ? 10.0*vc.getNegLog10PError() : VCFConstants.MISSING_QUALITY_v3_DOUBLE,
-                            vc.isFiltered() ? null : vc.getFilters(), vc.getAttributes());
+                            vc.isFiltered() ? vc.getFilters() : null, newAttributes);
                 }
 
+                if ( ! newContext.hasAttribute("FRI") ) {
+                    throw new StingException("FRI for fixed base not propagated. vc="+vc.toString());
+                }
                 out.add(newContext,ref.getBase());
+                return 1;
 
             } else {
                 out.add(vc,ref.getBase());
@@ -100,9 +111,12 @@ public class FixRefBases extends RodWalker<Integer,Integer> {
     }
 
     private VariantContext flipBases(VariantContext vc, ReferenceContext ref) {
+        logger.info(String.format("Flipping bases at variant position %s:%d",vc.getChr(),vc.getStart()));
         HashSet<Allele> newAlleles = new HashSet<Allele>(vc.getAlleles().size());
         newAlleles.add(Allele.create(ref.getBase(),true));
         newAlleles.add(Allele.create(vc.getReference().getBases()[0],false));
+        Map<String,Object> attribs = new HashMap<String,Object>(vc.getAttributes());
+        attribs.put("FRI",String.format("Flipped%s-%s",vc.getReference().toString(),Allele.create(ref.getBase(),true).toString()));
         for ( Allele a : vc.getAlternateAlleles() ) {
             if ( a.getBases()[0] != ref.getBase() ) {
                 newAlleles.add(a);
@@ -112,9 +126,8 @@ public class FixRefBases extends RodWalker<Integer,Integer> {
         VariantContext newVC = new VariantContext("FixRefBasesVC", ref.getLocus().getContig(),
                 ref.getLocus().getStart(), ref.getLocus().getStop(), newAlleles, flipGenotypes(vc.getGenotypes(),newAlleles),
                 vc.hasNegLog10PError() ? 10.0*vc.getNegLog10PError() : VCFConstants.MISSING_QUALITY_v3_DOUBLE,
-                vc.isFiltered() ? null : vc.getFilters(), vc.getAttributes());
+                vc.isFiltered() ? vc.getFilters() : null, attribs);
 
-        Map<String,Object> attribs = new HashMap<String,Object>(newVC.getAttributes());
         VariantContextUtils.calculateChromosomeCounts(newVC,attribs,false);
         VariantContext.modifyAttributes(newVC,attribs);
         return newVC;

java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java

@@ -29,7 +29,7 @@ public class
         String extraArgs = "-L 1:1-10,000,000";
         for (String tests : testsEnumerations) {
             WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -o %s",
-                    1, Arrays.asList("158ac8e6d32eb2ea1bbeebfa512965de"));
+                    1, Arrays.asList("8a0203f0533b628ad7f1f230a43f105f"));
             executeTestParallel("testSelect1", spec);
             //executeTest("testSelect1", spec);
         }
@@ -39,7 +39,7 @@ public class
     public void testSelect2() {
         String extraArgs = "-L 1:1-10,000,000";
         WalkerTestSpec spec = new WalkerTestSpec( withSelect(withSelect(root, "DP < 50", "DP50"), "set==\"Intersection\"", "intersection") + " " + extraArgs + " -o %s",
-                1, Arrays.asList("cee96f61ffa1d042fe0c63550c508ec9"));
+                1, Arrays.asList("a55653980b750fdc8396eecb00e3b18c"));
         executeTestParallel("testSelect2", spec);
         //executeTest("testSelect2", spec);
     }
@@ -60,8 +60,8 @@ public class
     @Test
     public void testVESimple() {
         HashMap<String, String> expectations = new HashMap<String, String>();
-        expectations.put("-L 1:1-10,000,000", "ff8c4ba16c7c14b4edbaf440f20641f9");
+        expectations.put("-L 1:1-10,000,000", "6c9a12fdd62672b69b2ed4f0bc7e8f97");
-        expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0 -E MendelianViolationEvaluator", "9b509ce5d31658eb09bb9597799b2908");
+        expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0 -E MendelianViolationEvaluator", "6a52a6454121974b71d9cfe2dad68c28");
 
         for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
             String extraArgs = entry.getKey();
@@ -84,10 +84,10 @@ public class
                 " -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
 
 
-        String matchingMD5 = "1e6d6e152c9a90513dd5b6eaa3729388";
+        String matchingMD5 = "7a8183402fe29f9c62c3c3cc4d45b46e";
         expectations.put("", matchingMD5);
         expectations.put(" -known comp_hapmap -known dbsnp", matchingMD5);
-        expectations.put(" -known comp_hapmap", "d28dd504017f39a91cde8e6f096879d6");
+        expectations.put(" -known comp_hapmap", "519b590635b7de035f8d5971115b47ba");
         for (String tests : testsEnumerations) {
             for (Map.Entry<String, String> entry : expectations.entrySet()) {
                 String extraArgs2 = entry.getKey();
@@ -124,7 +124,7 @@ public class
         for (String tests : testsEnumerations) {
             WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s -NO_HEADER",
                     2,
-                    Arrays.asList("6b97a019402b3984fead9a4e8b7c7c2a", "989bc30dea6c8a4cf771cd1b9fdab488"));
+                    Arrays.asList("50321436a65ef7d574286cb0a1c55f7e", "989bc30dea6c8a4cf771cd1b9fdab488"));
             executeTestParallel("testVEWriteVCF", spec);
             //executeTest("testVEWriteVCF", spec);
         }

scala/qscript/chartl/omni_qc.q

@@ -24,17 +24,21 @@ class omni_qc extends QScript {
   var august_calls_EUR = new TaggedFile("/humgen/1kg/processing/release/august/EUR.vcf","vcf")
   var august_calls_ASN = new TaggedFile("/humgen/1kg/processing/release/august/ASN.vcf","vcf")
   var august_calls_AFR = new TaggedFile("/humgen/1kg/processing/release/august/AFR.vcf","vcf")
-  var august_calls_EUR_refined = new TaggedFile("/humgen/1kg/processing/release/august/EUR.beagle.vcf.gz","vcf")
+  var august_calls_EUR_refined = new TaggedFile("/humgen/1kg/processing/release/august/bgzip_for_release/EUR.beagle.vcf.gz","vcf")
-  var august_calls_ASN_refined = new TaggedFile("/humgen/1kg/processing/release/august/ASN.beagle.vcf.gz","vcf")
+  var august_calls_ASN_refined = new TaggedFile("/humgen/1kg/processing/release/august/bgzip_for_release/ASN.beagle.vcf.gz","vcf")
-  var august_calls_AFR_refined = new TaggedFile("/humgen/1kg/processing/release/august/AFR.beagle.vcf.gz","vcf")
+  var august_calls_AFR_refined = new TaggedFile("/humgen/1kg/processing/release/august/bgzip_for_release/AFR.beagle.vcf.gz","vcf")
   var hiseq_calls_vcf = new TaggedFile("/humgen/gsa-scr1/chartl/projects/omni/resources/NA12878.HiSeq.v9.b36.vcf.gz","vcf")
   var pilot1_with_na12878_vcf = new TaggedFile("/humgen/1kg/analysis/bamsForDataProcessingPapers/lowpass_b36/calls/v2/N60/lowpass.N60.recal.mG6.retranche.vcf","vcf")
+  var pilot1_na12878_beagle = new File("/humgen/1kg/analysis/bamsForDataProcessingPapers/lowpass_b36/calls/beagle/lowpass.N60.recal.CEUTSI.bgl.output.vcf")
   //var august_calls_other_genotypes = _
 
   // OMNI VCF FILES
   var OMNI_b36_vcf = new TaggedFile("/humgen/illumina/1kg_seq_vcfs/Illumina_HapMap_Omni_2.5_764samples.vcf","vcf")
   var OMNI_b37_vcf = new TaggedFile("/broad/shptmp/chartl/Omni_2.5_764_samples.b37.deduped.vcf","vcf")
   var OMNI_hapmap_b36_vcf = new TaggedFile("/humgen/gsa-scr1/chartl/projects/omni/resources_oct7/Omni_2_5_pilot.b36.vcf","vcf")
+  var OMNI_b36_panel_vcf = new TaggedFile("/broad/shptmp/chartl/omni/vcfs/Omni_b36_with_panel_sets.vcf","vcf")
+  var OMNI_b37_birdseed = new File("/humgen/gsa-scr1/chartl/projects/omni/resources_oct7/OMNI_birdseed_only.vcf")
+  var OMNI_b37_joint = new File("/humgen/gsa-scr1/chartl/projects/omni/resources_oct7/OMNI_joint_birdseed_lowpass.vcf")
 
   // INTERVALS
   var pilot3_interval_list: String = "/humgen/gsa-hpprojects/1kg/1kg_pilot3/documents/CenterSpecificTargetLists/results/p3overlap.targets.b36.interval_list"
@@ -52,6 +56,14 @@ class omni_qc extends QScript {
   val scratch_dir = analysis_dir + "scratch/"
   val eval_dir = analysis_dir + "eval/"
   val vcf_dir = analysis_dir + "vcfs/"
+  val p1_ceu_only = scratch_dir+"Pilot1_CEU_only_sites.intervals.list"
+  val p1_chbjpt_only = scratch_dir+"Pilot1_CHBJPT_only_sites.intervals.list"
+  val p1_yri_only = scratch_dir+"Pilot1_YRI_only_sites.intervals.list"
+
+  // OTHER CHIPS
+
+  val OMNI_QUAD_1KG = new File("/humgen/gsa-scr1/chartl/projects/omni/resources_oct7/other_chips/1KG_OMNI.ref_fixed.vcf")
+  val AFFY_6_0 = new File("/humgen/gsa-scr1/chartl/projects/omni/resources_oct7/other_chips/1KG_ARRAY.ref_fixed.vcf")
 
   trait OmniArgs extends CommandLineGATK {
     this.jarFile = new File("/humgen/gsa-scr1/chartl/sting/dist/GenomeAnalysisTK.jar")
@@ -128,12 +140,15 @@ class omni_qc extends QScript {
     fix_421.variantVCF = OMNI_hapmap_b36_vcf
     fix_421.reference_sequence = b36_ref
     fix_421.out = new File(vcf_dir+swapExt(OMNI_hapmap_b36_vcf.getName,".vcf",".ref_fixed.vcf"))
+    fix_421.bypassException = true
     fix_764.variantVCF = OMNI_b36_vcf
     fix_764.reference_sequence = b36_ref
     fix_764.out = new File(vcf_dir+swapExt(OMNI_b36_vcf.getName,".vcf",".ref_fixed.vcf"))
+    fix_764.bypassException = true
     fix_764_b37.variantVCF = OMNI_b37_vcf
     fix_764_b37.reference_sequence = b37_ref
     fix_764_b37.out = new File(vcf_dir+swapExt(OMNI_b37_vcf.getName,".vcf",".ref_fixed.vcf"))
+    fix_764_b37.bypassException = true
     
     add(fix_421,fix_764,fix_764_b37)
 
@@ -142,24 +157,25 @@ class omni_qc extends QScript {
     var annotate_764 = new VariantAnnotator with OmniArgs
     var annotate_764_b37 = new VariantAnnotator with OmniArgs
 
-    annotate_421.variantVCF = fix_421.out
+    annotate_421.variantVCF = OMNI_hapmap_b36_vcf
     annotate_421.reference_sequence = b36_ref
     annotate_421.annotation :+= "ChromosomeCounts"
-    annotate_421.out = new File(vcf_dir+swapExt(fix_421.out.getName,".vcf",".annot.vcf"))
+    annotate_421.out = new File(vcf_dir+swapExt(annotate_421.variantVCF.getName,".vcf",".annot.vcf"))
-    annotate_764.variantVCF = fix_764.out
+    annotate_764.variantVCF = OMNI_b36_vcf
     annotate_764.reference_sequence = b36_ref
     annotate_764.annotation :+= "ChromosomeCounts"
-    annotate_764.out = new File(vcf_dir+swapExt(fix_764.out.getName,".vcf",".annot.vcf"))
+    annotate_764.out = new File(vcf_dir+swapExt(annotate_764.variantVCF.getName,".vcf",".annot.vcf"))
-    annotate_764_b37.variantVCF = fix_764_b37.out
+    annotate_764_b37.variantVCF = OMNI_b37_vcf
     annotate_764_b37.reference_sequence = b37_ref
     annotate_764_b37.annotation :+= "ChromosomeCounts"
-    annotate_764_b37.out = new File(vcf_dir+swapExt(fix_764_b37.out.getName,".vcf",".annot.vcf"))
+    annotate_764_b37.out = new File(vcf_dir+swapExt(annotate_764_b37.variantVCF.getName,".vcf",".annot.vcf"))
 
     add(annotate_421,annotate_764,annotate_764_b37)
 
     /** Eval the omni chip against the various comps **/
     runEval(annotate_764.out,gunzip_p1_ceu.outFile,"OMNI_764","Pilot1_CEU",pilot1_interval_list, b36_ref)
-    runEval(annotate_421.out,gunzip_p1_ceu.outFile,"OMNI_421","Pilot1_CEU",pilot1_interval_list, b36_ref)
+    runEval(annotate_421.out,gunzip_p1_ceu.outFile,"OMNI_421","Pilot1_CEU",pilot1_interval_list, b36_ref,true)
+    //runEval(OMNI_hapmap_b36_vcf,gunzip_p1_ceu.outFile,"OMNI_421_Unfixed","Pilot1_CEU",pilot1_interval_list,b36_ref)
     runEval(annotate_764.out,gunzip_p1_chb.outFile,"OMNI_764","Pilot1_CHB",pilot1_interval_list, b36_ref)
     runEval(annotate_421.out,gunzip_p1_chb.outFile,"OMNI_421","Pilot1_CHB",pilot1_interval_list, b36_ref)
     runEval(annotate_764.out,gunzip_p1_yri.outFile,"OMNI_764","Pilot1_YRI",pilot1_interval_list, b36_ref)
@@ -170,7 +186,13 @@ class omni_qc extends QScript {
     runEval(annotate_764_b37.out,gunzip_ag_asn.outFile,"OMNI_764","August_ASN",production_interval_list, b37_ref)
     runEval(annotate_764_b37.out,gunzip_ag_afr.outFile,"OMNI_764","Ausust_AFR",production_interval_list, b37_ref)
     runEval(annotate_764.out,gunzip_hiseq.outFile,"OMNI_764","HiSeq",hiseq_interval_list, b36_ref)
-    runEval(annotate_764.out,OMNI_hapmap_b36_vcf,"OMNI_764","OMNI_421",pilot1_interval_list,b36_ref)
+    runEval(annotate_764.out,annotate_421.out,"OMNI_764","OMNI_421_FIXED",pilot1_interval_list,b36_ref)
+    runEval(annotate_764.out,OMNI_QUAD_1KG,"OMNI_764","OMNI_QUAD",pilot1_interval_list,b36_ref)
+    runEval(annotate_764.out,AFFY_6_0,"OMNI_764","AFFY_6_0",pilot1_interval_list,b36_ref)
+    runEval(OMNI_b37_birdseed,gunzip_ag_eur.outFile,"OMNI_birdseed","August_EUR",production_interval_list,b37_ref)
+    runEval(OMNI_b37_joint,gunzip_ag_eur.outFile,"OMNI_joint","August_EUR",production_interval_list,b37_ref)
+    runEval(OMNI_QUAD_1KG,gunzip_p1_ceu.outFile,"OMNI_QUAD_1KG","Pilot1_CEU",pilot1_interval_list,b36_ref)
+    runEval(AFFY_6_0,gunzip_p1_ceu.outFile,"AFFY_6_0","Pilot1_CEU",pilot1_interval_list,b36_ref)
 
     var eval1KG_exclude = new VariantEval with OmniArgs
     eval1KG_exclude.samples :+= "/broad/shptmp/chartl/omni/scratch/OMNI_764_vs_Pilot3.sample_overlap.exclude.mixups.txt"
@@ -187,6 +209,31 @@ class omni_qc extends QScript {
 
     runAFComparison(annotate_764.out, gunzip_p1_ceu.outFile, gunzip_p1_chb.outFile, gunzip_p1_yri.outFile)
 
+    var subset421: SelectVariants = new SelectVariants with OmniArgs
+    subset421.reference_sequence = b36_ref
+    subset421.sample :+= (new File(scratch_dir+"OMNI_421_vs_Pilot1_CEU.sample_overlap.txt")).getAbsolutePath
+    subset421.variantVCF = annotate_764.out
+    subset421.out = new File(vcf_dir+swapExt(annotate_764.out.getName,".vcf",".subset.pilot1CEU.vcf"))
+
+    add(subset421)// lastly to find things in the three-way pilot venn
+
+    var combine: CombineVariants = new CombineVariants with OmniArgs
+    combine.reference_sequence = b36_ref
+    combine.rodBind :+= new RodBind("CEU","VCF",gunzip_p1_ceu.outFile)
+    combine.rodBind :+= new RodBind("ASN","VCF",gunzip_p1_chb.outFile)
+    combine.rodBind :+= new RodBind("YRI","VCF",gunzip_p1_yri.outFile)
+    combine.genotypeMergeOptions = Some(VariantContextUtils.GenotypeMergeType.UNIQUIFY)
+    combine.priority = "%s,%s,%s".format("CEU","ASN","YRI")
+    combine.out = new File(vcf_dir+"Pilot1_Populations_Combined.vcf")
+
+    add(combine)
+
+    selectSites(OMNI_b36_panel_vcf,p1_ceu_only,"ceu_only_sites")
+    selectSites(OMNI_b36_panel_vcf,p1_chbjpt_only,"chbjpt_only_sites")
+    selectSites(OMNI_b36_panel_vcf,p1_yri_only,"yri_only_sites")
+
+    runBeagleAnalysis(new File(vcf_dir + "Illumina_HapMap_Omni_2.5_764samples.annot.stripped.vcf"))
+
   }
 
   def processAuxiliaryChipData(otherChips: File) : List[(String,File)] = {
@@ -194,7 +241,7 @@ class omni_qc extends QScript {
     return Nil
   }
 
-  def runEval(eval: File, comp: File, eBase: String, cBase: String, intervals: String, reference: File) = {
+  def runEval(eval: File, comp: File, eBase: String, cBase: String, intervals: String, reference: File, interesting: Boolean = false) = {
     var base = "%s_vs_%s".format(eBase,cBase)
     var getOverlap = new GetSampleOverlap
     getOverlap.in_vcfs :+= eval
@@ -214,6 +261,11 @@ class omni_qc extends QScript {
 
     vEval.out = new File(eval_dir+base+".eval.csv")
 
+    if ( interesting ) {
+      vEval.discordantInteresting = true
+      vEval.outputVCF = new File(vcf_dir+"%s_vs_%s.interesting_sites.vcf".format(eBase,cBase))
+    }
+
     add(vEval)
 
   }
@@ -257,6 +309,20 @@ class omni_qc extends QScript {
     runComps("EUR",nameToSubset("EUR").out,"ASW",nameToSubset("ASW").out)
     runComps("EUR",nameToSubset("EUR").out,"AMR",nameToSubset("ADM").out)
 
+
+    var panelCombine: CombineVariants = new CombineVariants with OmniArgs
+    panelCombine.reference_sequence = b36_ref
+    panelCombine.priority = ""
+    for ( p <- panels ) {
+      panelCombine.rodBind :+= new RodBind(p,"VCF",nameToSubset(p).out)
+      panelCombine.priority = if ( panelCombine.priority.equals("") ) p else panelCombine.priority + "," + p
+    }
+    panelCombine.out = OMNI_b36_panel_vcf
+    panelCombine.genotypeMergeOptions = Some(VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE)
+    panelCombine.variantMergeOptions = Some(VariantContextUtils.VariantMergeType.UNION)
+    panelCombine.setKey = "panel"
+
+    add(panelCombine)
     return true
 
   }
@@ -282,6 +348,8 @@ class omni_qc extends QScript {
     eval.rodBind :+= new RodBind("comp%s".format(cBase),"VCF",compVCF)
     eval.noStandard = true
     eval.E :+= "AlleleFrequencyComparison"
+    eval.reportType = Some(VE2TemplateType.CSV)
+    eval.out = new File(eval_dir+"%s_vs_%s_allele_frequency.eval".format(eBase,cBase))
 
     add(eval)
 
@@ -293,7 +361,147 @@ class omni_qc extends QScript {
     combine.genotypeMergeOptions = Some(VariantContextUtils.GenotypeMergeType.UNIQUIFY)
     combine.priority = "%s,%s".format(eBase,cBase)
 
-    add(combine)
+    //add(combine)
 
   }
+
+  def selectSites(vcf: File, intervals: String, base: String) {
+    var sv = new SelectVariants with OmniArgs
+    sv.reference_sequence = b36_ref
+    sv.variantVCF = vcf
+    sv.out = swapExt(vcf,".vcf",base+".vcf")
+    sv.intervalsString :+= intervals
+
+    add(sv)
+  }
+
+  def runBeagleAnalysis(omnivcf: File) {
+    var combine : CombineVariants  = new CombineVariants with OmniArgs
+    combine.reference_sequence = b36_ref
+    for ( c <- 1 until 23) {
+      combine.rodBind :+= new RodBind("beagle%s".format(c),"VCF",runBeagle(omnivcf,"%s".format(c)))
+      if ( c > 1 ) {
+        combine.priority = combine.priority+",%s%s".format("beagle",c)
+      } else {
+        combine.priority = "%s%s".format("beagle",c)
+      }
+    }
+    combine.genotypeMergeOptions = Some(VariantContextUtils.GenotypeMergeType.PRIORITIZE)
+    combine.variantMergeOptions = Some(VariantContextUtils.VariantMergeType.UNION)
+
+    combine.out = swapExt(pilot1_with_na12878_vcf,".vcf",".beagle_refined_with_omni.vcf")
+
+    add(combine)
+
+    var select : SelectVariants = new SelectVariants with OmniArgs
+    select.reference_sequence = b36_ref
+    select.variantVCF = combine.out
+    select.sample :+= "NA12878"
+    select.out = new File(vcf_dir + "NA12878.lowpass.beagle.refined.with.pilot1.vcf")
+
+    add(select)
+
+    var eval : VariantEval = new VariantEval with OmniArgs
+    eval.reference_sequence = b36_ref
+    eval.rodBind :+= new RodBind("evalNA12878LowPass","VCF",select.out)
+    eval.rodBind :+= new RodBind("compNA12878HiSeq","VCF",hiseq_calls_vcf)
+    eval.E :+= "GenotypeConcordance"
+    eval.out = new File(eval_dir+"NA12878.lowpass.beagle.vs.HiSeq.eval")
+    eval.excludeIntervals :+= new File(pilot1_interval_list)
+    eval.reportType = Some(VE2TemplateType.CSV)
+
+    add(eval)
+
+    var eval2: VariantEval = new VariantEval with OmniArgs
+    eval2.reference_sequence = b36_ref
+    eval2.rodBind :+= new RodBind("evalNA12878Beagle","VCF",pilot1_na12878_beagle)
+    eval2.rodBind :+= new RodBind("compNA12878HiSeq","VCF",hiseq_calls_vcf)
+    eval2.E :+= "GenotypeConcordance"
+    eval2.sample :+= "NA12878"
+    eval2.out = new File(eval_dir+"NA12878.lowpass.nochip.vs.Hiseq.eval")
+    eval2.excludeIntervals :+= new File(pilot1_interval_list)
+    eval2.reportType = Some(VE2TemplateType.CSV)
+
+    add(eval2)
+
+    var eval3: VariantEval = new VariantEval with OmniArgs
+    eval3.reference_sequence = b36_ref
+    eval3.rodBind :+= new RodBind("evalNA12878NoBeagle","VCF",pilot1_with_na12878_vcf)
+    eval3.rodBind :+= new RodBind("compNA12878HiSeq","VCF",hiseq_calls_vcf)
+    eval3.E :+= "GenotypeConcordance"
+    eval3.sample :+= "NA12878"
+    eval3.out = new File(eval_dir+"NA12878.lowpass.nochip.norefined.vs.Hiseq.eval")
+    eval3.excludeIntervals :+= new File(pilot1_interval_list)
+    eval3.reportType = Some(VE2TemplateType.CSV)
+
+    add(eval3)
+  }
+
+  def runBeagle(omnivcf: File, chr: String): File = {
+    var beagleInput = new ProduceBeagleInput with OmniArgs
+    beagleInput.reference_sequence = b36_ref
+    beagleInput.intervalsString :+= chr
+    beagleInput.variantVCF = pilot1_with_na12878_vcf
+    beagleInput.rodBind :+= new RodBind("validation","VCF",omnivcf)
+    beagleInput.validation_genotype_ptrue = Some(0.99)
+    beagleInput.out = new File(scratch_dir+"/"+swapExt(beagleInput.variantVCF.getName,".vcf",".%s.beagle".format(chr)))
+    println (beagleInput.out.getAbsolutePath)
+
+    var runBeagle : BeagleRefinement = new BeagleRefinement
+    runBeagle.beagleInput = beagleInput.out
+    runBeagle.beagleOutputBase = "Pilot1_NA12878_Beagle_with_OMNI_chr%s".format(chr)
+    runBeagle.beagleMemoryGigs = 6
+    runBeagle.memoryLimit = Some(6)
+    runBeagle.beagleOutputDir = ""
+    runBeagle.freezeOutputs
+
+    var gunzipPhased = new GunzipFile
+    gunzipPhased.gunzipMe = runBeagle.beaglePhasedFile
+    gunzipPhased.outFile = new File(scratch_dir+swapExt(runBeagle.beaglePhasedFile.getName,".gz",""))
+
+    var gunzipLike = new GunzipFile
+    gunzipLike.gunzipMe = runBeagle.beagleLikelihoods
+    gunzipLike.outFile = new File(scratch_dir+swapExt(runBeagle.beagleLikelihoods.getName,".gz",""))  
+
+
+    var convertBack : BeagleOutputToVCF = new BeagleOutputToVCF with OmniArgs
+    convertBack.reference_sequence = b36_ref
+    convertBack.variantVCF = pilot1_with_na12878_vcf
+    convertBack.intervalsString :+= chr
+    convertBack.rodBind :+= new RodBind("beagleR2","beagle",runBeagle.beagleRSquared)
+    convertBack.rodBind :+= new RodBind("beagleProbs","beagle",gunzipLike.outFile)
+    convertBack.rodBind :+= new RodBind("beaglePhased","beagle",gunzipPhased.outFile)
+    convertBack.out = new File(vcf_dir+swapExt(pilot1_with_na12878_vcf.getName,".vcf",".chr%s.beagle_refined_plus_omni.vcf".format(chr)))
+
+    add(beagleInput,runBeagle,gunzipPhased,gunzipLike,convertBack)
+
+    return convertBack.out
+  }
+
+  class BeagleRefinement extends CommandLineFunction {
+    @Input(doc="The beagle input file") var beagleInput: File = _
+    var beagleOutputBase: String = _
+    var beagleMemoryGigs: Int = 4
+
+    /**
+     * Note: These get set
+     */
+    @Output(doc="The beagle phased file") var beaglePhasedFile: File = _
+    @Output(doc="The beagle likelihood file") var beagleLikelihoods: File = _
+    @Output(doc="The beagle r2 file") var beagleRSquared: File = _
+    var beagleOutputDir: String = _
+
+    def freezeOutputs = {
+      if ( beagleOutputDir == null && beagleInput.getParent == null ) {
+        beagleOutputDir = ""
+      } else if ( beagleOutputDir == null ) {
+        beagleOutputDir = beagleInput.getParent+"/"
+      }
+      beaglePhasedFile = new File(beagleOutputDir+beagleOutputBase+"."+beagleInput.getName+".phased.gz")
+      beagleLikelihoods = new File(beagleOutputDir+beagleOutputBase+"."+beagleInput.getName+".gprobs.gz")
+      beagleRSquared = new File(beagleOutputDir+beagleOutputBase+"."+beagleInput.getName+".r2")
+    }
+
+    def commandLine = "java -Djava.io.tmpdir=%s -Xmx%dg -jar /humgen/gsa-hpprojects/software/beagle/beagle.jar like=%s out=%s".format(beagleInput.getParent,beagleMemoryGigs,beagleInput.getAbsolutePath,beagleOutputBase)
+  }
 }