Adjusted Genotype concordance to more accurately use the new Genotyping code, fixed the VCF rod, and temp. fix the build by reintroducing Shermans ReadCigarFormatter

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1745 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java

@@ -34,6 +34,12 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
         super(name);
     }
 
+    private RodVCF(String name, VCFRecord currentRecord, VCFReader reader) {
+        super(name);
+        mCurrentRecord = currentRecord;
+        mReader = reader;
+    }
+
     public void assertNotNull() {
         if (mCurrentRecord == null) {
             throw new UnsupportedOperationException("The current Record is null");
@@ -46,9 +52,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
     }
 
     public Object initialize(final File source) throws FileNotFoundException {
-        if (mReader == null) {
+        if (mReader == null) mReader = new VCFReader(source);
-            mReader = new VCFReader(source);
-        }
         return mReader.getHeader();
     }
 
@@ -60,7 +64,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
             return "";
     }
 
-    public Iterator<RodVCF> createIterator(String name, File file) {
+    public static RodVCF createIterator(String name, File file) {
         RodVCF vcf = new RodVCF(name);
         try {
             vcf.initialize(file);
@@ -155,7 +159,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
     @Override
     public GenomeLoc getLocation() {
         this.assertNotNull();
-        return GenomeLocParser.createGenomeLoc(mCurrentRecord.getChromosome(), mCurrentRecord.getPosition());
+        return GenomeLocParser.createGenomeLoc(mCurrentRecord.getChromosome(), mCurrentRecord.getPosition(), mCurrentRecord.getPosition());
     }
 
     /**
@@ -202,7 +206,8 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
      */
     @Override
     public String getAlternateBases() {
-        if (!this.isBiallelic()) throw new UnsupportedOperationException("We're not biallelic, so please call getAlternateBaseList instead");
+        if (!this.isBiallelic())
+            throw new UnsupportedOperationException("We're not biallelic, so please call getAlternateBaseList instead");
         return this.mCurrentRecord.getAlternateAlleles().get(0);
     }
 
@@ -341,7 +346,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
     @Override
     public RodVCF next() {
         mCurrentRecord = mReader.next();
-        return this;
+        return new RodVCF(this.name, mCurrentRecord, mReader);
     }
 
     @Override

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/ReadCigarFormatter.java

@@ -0,0 +1,76 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+
+package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
+
+/**
+ * Returns formatted read given read string and cigar string
+ * Essentially removes header bases, soft clipped bases, and currently removes insertions
+ * Deletions coded as "D"
+ *
+ * @author shermanjia
+ */
+
+public class ReadCigarFormatter {
+    public String FormatRead(String cigar, String read){
+        // returns a cigar-formatted sequence (removes insertions, inserts 'D' to where deletions occur
+        String formattedRead = ""; char c; String count;
+        int cigarPlaceholder = 0; int subcigarLength = 0;
+        int readPlaceholder = 0; int subreadLength = 0;
+
+        //reads cigar string
+        for (int i = 0; i < cigar.length(); i++){
+            c = cigar.charAt(i);
+            if (c == 'M'){
+                //If reach M for match/mismatch, get number immediately preceeding 'M' and tack on that many characters to sequence
+                subcigarLength = i-cigarPlaceholder;
+                count = cigar.substring(cigarPlaceholder, i);
+
+                subreadLength = Integer.parseInt(count);
+                formattedRead = formattedRead + read.substring(readPlaceholder, readPlaceholder+subreadLength);
+
+                //increment placeholders
+                cigarPlaceholder = i+1;
+                readPlaceholder = readPlaceholder + subreadLength;
+            } else if (c == 'I'){
+                //***NOTE: To be modified later if needed (insertions removed here)***
+
+                //If reaches I for insertion, get number before 'I' and skip that many characters in sequence
+                count = cigar.substring(cigarPlaceholder, i);
+                subreadLength = Integer.parseInt(count);
+
+                //increment placeholders without adding inserted bases to sequence (effectively removes insertion).
+                cigarPlaceholder = i+1;
+                readPlaceholder = readPlaceholder + subreadLength;
+            } else if (c == 'H' || c == 'S'){
+                //(H = Headers or S = Soft clipped removed here)***
+
+                //If reaches H for insertion, get number before 'H' and skip that many characters in sequence
+                count = cigar.substring(cigarPlaceholder, i);
+                subreadLength = Integer.parseInt(count);
+
+                //increment cigar placeholder without adding inserted bases to sequence (effectively removes insertion).
+                cigarPlaceholder = i+1;
+            } else if (c == 'D'){
+                //If reaches D for deletion, insert 'D' into sequence as placeholder
+                count = cigar.substring(cigarPlaceholder, i);
+                subreadLength = Integer.parseInt(count);
+
+                //Add one 'D' for each deleted base
+                String deletion = "";
+                for (int j = 1; j <= subreadLength; j++){
+                    deletion = deletion + "D";
+                }
+
+                //update placeholders
+                formattedRead = formattedRead + deletion;
+                cigarPlaceholder = i+1;
+            }
+
+        }
+        return formattedRead;
+    }
+
+}

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

@@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
+import org.broadinstitute.sting.utils.genotype.Genotype;
 import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
 import org.broadinstitute.sting.utils.genotype.Variation;
 
@@ -51,25 +51,30 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
             throw new StingException("Failure: trying to analyze genotypes of non-genotype data");
 
         // This shouldn't happen, but let's check anyways
-	if ( BaseUtils.simpleBaseToBaseIndex(ref) == -1 )
+        if (BaseUtils.simpleBaseToBaseIndex(ref) == -1)
             return;
 
-        DiploidGenotype g = DiploidGenotype.createHomGenotype(ref);
+        // get the genotyping data
+        Genotype chipGenotype = null;
+        Genotype evalGenotype = null;
+        if (chip != null) chipGenotype = ((VariantBackedByGenotype)chip).getCalledGenotype();
+        if (eval != null) evalGenotype = ((VariantBackedByGenotype)eval).getCalledGenotype();
+
         int truthIndex, callIndex;
         if (chip == null)
             truthIndex = UNKNOWN;
-        else if (chip.getAlternateBases().equals(g.toString()))
+        else if (!chipGenotype.isVariant(ref))
             truthIndex = REF;
-        else if (chip.getAlternateBases().charAt(0) != chip.getAlternateBases().charAt(1))
+        else if (chipGenotype.isHet())
             truthIndex = VAR_HET;
         else
             truthIndex = VAR_HOM;
 
         if (eval == null)
             callIndex = NO_CALL;
-        else if (eval.getAlternateBases().equals(g.toString()))
+        else if (!evalGenotype.isVariant(ref))
             callIndex = REF;
-        else if (eval.getAlternateBases().charAt(0) != eval.getAlternateBases().charAt(1))
+        else if (evalGenotype.isHet())
             callIndex = VAR_HET;
         else
             callIndex = VAR_HOM;
@@ -84,7 +89,7 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
 
     public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
         Variation chip = (Variation) tracker.lookup(dbName, null);
-	if ( eval != null || chip != null )
+        if (eval != null || chip != null)
             inc(chip, eval, ref);
         return null;
     }
@@ -102,9 +107,7 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
         s.add(sb.toString());
     }
 
-    /**
+    /** How many overall calls where made that aren't NO_CALLS or UNKNOWNS? */
-     * How many overall calls where made that aren't NO_CALLS or UNKNOWNS?
-     */
     private int getNCalled() {
         int n = 0;
         for (int i = 0; i < 4; i++)