part two: todo's in combine variants, fixes for InferredGeneticContext, and some other tests and clean-up.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3721 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broad/tribble/vcf/VCFCompoundHeaderLine.java

@@ -7,7 +7,7 @@ import java.util.Map;
 /**
  * a base class for compound header lines, which include info lines and format lines (so far)
  */
-public abstract class VCFCompoundHeaderLine extends VCFHeaderLine {
+public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCFNamedHeaderLine {
     public enum SupportedHeaderLineType {
         INFO(true), FORMAT(false);
 

java/src/org/broad/tribble/vcf/VCFFilterHeaderLine.java

@@ -9,7 +9,7 @@ import java.util.Map;
  * @author ebanks
  * A class representing a key=value entry for FILTER fields in the VCF header
  */
-public class VCFFilterHeaderLine extends VCFHeaderLine {
+public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeaderLine  {
 
     private String name;
     private String description;

java/src/org/broad/tribble/vcf/VCFHeaderLineType.java

@@ -9,7 +9,7 @@ public enum VCFHeaderLineType {
     public Object convert(String value, VCFCompoundHeaderLine.SupportedHeaderLineType hlt) {
         switch (this) {
             case Integer:
-                return java.lang.Integer.valueOf(value); // the java.lang is needed since we use Integer as a enum name
+                return Math.round(java.lang.Float.valueOf(value)); // this seems like we're allowing off spec values, but use it for now
             case Float:
                 return java.lang.Float.valueOf(value);
             case String:

java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/InferredGeneticContext.java

@@ -213,7 +213,7 @@ final class InferredGeneticContext {
 //        return selected;
 //    }
 
-    public String getAttributeAsString(String key)      { return (String)getAttribute(key); }
+    public String getAttributeAsString(String key)      { return (String.valueOf(getAttribute(key))); }
     public int getAttributeAsInt(String key)            { return (Integer)getAttribute(key); }
     public double getAttributeAsDouble(String key)      { return (Double)getAttribute(key); }
 

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

@@ -124,12 +124,12 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
                         if ( ! lineName.equals(otherName) )
                             throw new IllegalStateException("Incompatible header types: " + line + " " + other );
                     } else {
-                        //String lineName = ((VCFInfoHeaderLine) line).getName();
+                        String lineName = ((VCFCompoundHeaderLine) line).getName();
-                        //String otherName = ((VCFFilterHeaderLine) other).getName();
+                        String otherName = ((VCFCompoundHeaderLine) other).getName();
 
-                        // todo -- aaron, please complete these comparisons when INFO and Format header lines are made into one
+                        // if the names are the same, but the values are different, we need to quit
-                        //if ( (lineType != null && ! lineType.equals(otherType)) || (lineCount != null && !lineCounts.equals(otherCount)))
+                        if (lineName.equals(otherName) && !line.equals(other))
-                        //    throw new IllegalStateException("Incompatible header types: " + line + " " + other );
+                            throw new IllegalStateException("Incompatible header types, collision between these two types: " + line + " " + other );
                     }
                 } else {
                     map.put(key, line);

java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java

@@ -0,0 +1,102 @@
+package org.broadinstitute.sting.gatk.walkers.variantutils;
+
+import org.broad.tribble.vcf.VCFHeader;
+import org.broad.tribble.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.gatk.refdata.features.vcf4.VCF4Codec;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderUnitTest;
+import org.junit.Assert;
+import org.junit.Test;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+/**
+ * test out pieces of the combine variants code
+ */
+public class CombineVariantsUnitTest {
+
+    // this header is a small subset of the header in VCFHeaderUnitTest: VCF4headerStrings
+    public static String[] VCF4headerStringsSmallSubset = {
+                "##fileformat=VCFv4.0",
+                "##filedate=2010-06-21",
+                "##reference=NCBI36",
+                "##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">",
+                "##INFO=<ID=DP, Number=1, Type=Integer, Description=\"Total number of reads in haplotype window\">",
+                "##INFO=<ID=AF, Number=1, Type=Float, Description=\"Dindel estimated population allele frequency\">",
+                "##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">",
+                "##FORMAT=<ID=GT, Number=1, Type=String, Description=\"Genotype\">",
+                "##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">",
+                "##FORMAT=<ID=GQ, Number=1, Type=Integer, Description=\"Genotype quality\">",
+                };
+
+    // altered info field
+    public static String[] VCF4headerStringsBrokenInfo = {
+                "##fileformat=VCFv4.0",
+                "##filedate=2010-06-21",
+                "##reference=NCBI36",
+                "##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">",
+                "##INFO=<ID=DP, Number=1, Type=Integer, Description=\"Total number of reads in haplotype window\">",
+                "##INFO=<ID=AF, Number=1, Type=Integer, Description=\"Dindel estimated population allele frequency\">", // float to integer
+                "##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">",
+                "##FORMAT=<ID=GT, Number=1, Type=String, Description=\"Genotype\">",
+                "##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">",
+                "##FORMAT=<ID=GQ, Number=1, Type=Integer, Description=\"Genotype quality\">",
+                };
+
+    // altered format field
+    public static String[] VCF4headerStringsBrokenFormat = {
+                "##fileformat=VCFv4.0",
+                "##filedate=2010-06-21",
+                "##reference=NCBI36",
+                "##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">",
+                "##INFO=<ID=DP, Number=1, Type=Integer, Description=\"Total number of reads in haplotype window\">",
+                "##INFO=<ID=AF, Number=1, Type=Float, Description=\"Dindel estimated population allele frequency\">",
+                "##FILTER=<ID=NoQCALL, Description=\"Variant called by Dindel but not confirmed by QCALL\">",
+                "##FORMAT=<ID=GT, Number=6, Type=String, Description=\"Genotype\">", // changed 1 to 6 here
+                "##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">",
+                "##FORMAT=<ID=GQ, Number=1, Type=Integer, Description=\"Genotype quality\">",
+                };
+
+    private VCF4Codec createHeader(String[] headerStr) {
+        VCF4Codec codec = new VCF4Codec();
+        List<String> headerFields = new ArrayList<String>();
+        for (String str : headerStr)
+            headerFields.add(str);
+        Assert.assertEquals(headerStr.length+1 /* for the # line */,codec.createHeader(headerFields,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"));
+        return codec;
+    }
+
+    @Test
+    public void testHeadersWhereOneIsAStrictSubsetOfTheOther() {
+        VCFHeader one = createHeader(VCFHeaderUnitTest.VCF4headerStrings).getHeader(VCFHeader.class);
+        VCFHeader two = createHeader(VCF4headerStringsSmallSubset).getHeader(VCFHeader.class);
+        ArrayList<VCFHeader> headers = new ArrayList<VCFHeader>();
+        headers.add(one);
+        headers.add(two);
+        Set<VCFHeaderLine> lines = CombineVariants.smartMergeHeaders(headers);
+        Assert.assertEquals(VCFHeaderUnitTest.VCF4headerStrings.length,lines.size());
+    }
+
+    @Test(expected=IllegalStateException.class)
+    public void testHeadersInfoDifferentValues() {
+        VCFHeader one = createHeader(VCFHeaderUnitTest.VCF4headerStrings).getHeader(VCFHeader.class);
+        VCFHeader two = createHeader(VCF4headerStringsBrokenInfo).getHeader(VCFHeader.class);
+        ArrayList<VCFHeader> headers = new ArrayList<VCFHeader>();
+        headers.add(one);
+        headers.add(two);
+        Set<VCFHeaderLine> lines = CombineVariants.smartMergeHeaders(headers);
+        Assert.assertEquals(VCFHeaderUnitTest.VCF4headerStrings.length,lines.size());
+    }
+
+    @Test(expected=IllegalStateException.class)
+    public void testHeadersFormatDifferentValues() {
+        VCFHeader one = createHeader(VCFHeaderUnitTest.VCF4headerStrings).getHeader(VCFHeader.class);
+        VCFHeader two = createHeader(VCF4headerStringsBrokenFormat).getHeader(VCFHeader.class);
+        ArrayList<VCFHeader> headers = new ArrayList<VCFHeader>();
+        headers.add(one);
+        headers.add(two);
+        Set<VCFHeaderLine> lines = CombineVariants.smartMergeHeaders(headers);
+        Assert.assertEquals(VCFHeaderUnitTest.VCF4headerStrings.length,lines.size());
+    }
+}

java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java

@@ -21,45 +21,38 @@ import java.util.List;
  */
 public class VCFHeaderUnitTest extends BaseTest {
 
-    @Test
+    private VCF4Codec createHeader(String[] headerStr) {
-    public void testVCF4ToVCF3() {
         VCF4Codec codec = new VCF4Codec();
         List<String> headerFields = new ArrayList<String>();
-        for (String str : VCF3_3headerStrings)
+        for (String str : headerStr)
             headerFields.add(str);
-        Assert.assertEquals(17,codec.createHeader(headerFields,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"));
+        Assert.assertEquals(headerStr.length+1 /* for the # line */,codec.createHeader(headerFields,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"));
+        return codec;
+    }
+
+    @Test
+    public void testVCF4ToVCF3() {
+        VCF4Codec codec = createHeader(VCF4headerStrings);
         codec.getHeader(VCFHeader.class).setVersion(VCFHeaderVersion.VCF3_3);
         checkMD5ofHeaderFile(codec, "5873e029bd50d6836b86438bccd15456");
     }
 
     @Test
     public void testVCF4ToVCF3Alternate() {
-        VCF4Codec codec = new VCF4Codec();
+        VCF4Codec codec = createHeader(VCF4headerStrings_with_negitiveOne);
-        List<String> headerFields = new ArrayList<String>();
-        for (String str : VCF3_3headerStrings_with_negitiveOne)
-            headerFields.add(str);
-        Assert.assertEquals(17,codec.createHeader(headerFields,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"));
         codec.getHeader(VCFHeader.class).setVersion(VCFHeaderVersion.VCF3_3);
         checkMD5ofHeaderFile(codec, "e750fd0919704d10813dfe57ac1a0df3");
     }
 
     @Test
     public void testVCF4ToVCF4() {
-        VCF4Codec codec = new VCF4Codec();
+        VCF4Codec codec = createHeader(VCF4headerStrings);
-        List<String> headerFields = new ArrayList<String>();
-        for (String str : VCF3_3headerStrings)
-            headerFields.add(str);
-        Assert.assertEquals(17, codec.createHeader(headerFields, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"));
         checkMD5ofHeaderFile(codec, "4648aa1169257e0a8a9d30131adb5f35");
     }
 
     @Test
     public void testVCF4ToVCF4_alternate() {
-        VCF4Codec codec = new VCF4Codec();
+        VCF4Codec codec = createHeader(VCF4headerStrings_with_negitiveOne);
-        List<String> headerFields = new ArrayList<String>();
-        for (String str : VCF3_3headerStrings_with_negitiveOne)
-            headerFields.add(str);
-        Assert.assertEquals(17, codec.createHeader(headerFields, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"));
         checkMD5ofHeaderFile(codec, "ad8c4cf85e868b0261ab49ee2c613088");
     }
 
@@ -92,7 +85,7 @@ public class VCFHeaderUnitTest extends BaseTest {
     }
 
 
-    public String[] VCF3_3headerStrings = {
+    public static String[] VCF4headerStrings = {
                 "##fileformat=VCFv4.0",
                 "##filedate=2010-06-21",
                 "##reference=NCBI36",
@@ -111,7 +104,7 @@ public class VCFHeaderUnitTest extends BaseTest {
                 "##FORMAT=<ID=GQ, Number=1, Type=Integer, Description=\"Genotype quality\">",
                 };
 
-    public String[] VCF3_3headerStrings_with_negitiveOne = {
+    public static String[] VCF4headerStrings_with_negitiveOne = {
                 "##fileformat=VCFv4.0",
                 "##filedate=2010-06-21",
                 "##reference=NCBI36",