- Read in arguments for the header based on reflection

- Hook up Variation and Genotype in SSG



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2300 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PointEstimateGenotypeCalculationModel.java

@@ -72,7 +72,6 @@ public class PointEstimateGenotypeCalculationModel extends EMGenotypeCalculation
 
             // we can now create the genotype call object
             GenotypeCall call = GenotypeWriterFactory.createSupportedGenotypeCall(OUTPUT_FORMAT, ref, context.getLocation());
-            call.setVariation(null);
 
             if ( call instanceof ReadBacked ) {
                 ((ReadBacked)call).setPileup(discoveryGL.first);
@@ -97,7 +96,10 @@ public class PointEstimateGenotypeCalculationModel extends EMGenotypeCalculation
                     if ( dbsnp != null )
                         ((IDBacked)locusdata).setID(dbsnp.getRS_ID());
                 }
+                locusdata.setGenotypeCalls(Arrays.asList((Genotype)call));
             }
+            
+            call.setVariation(locusdata);
 
             return new Pair<VariationCall, List<Genotype>>(locusdata, Arrays.asList((Genotype)call));
         }

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -33,15 +33,14 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator;
 import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.Window;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.cmdLine.*;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentCollection;
 import org.broadinstitute.sting.utils.genotype.*;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
 
 import java.io.File;
 import java.util.*;
+import java.lang.reflect.Field;
 
 
 @Reference(window=@Window(start=-20,stop=20))
@@ -173,24 +172,18 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
         if ( !UAC.NO_SLOD )
             headerInfo.add("INFO=SB,1,Float,\"Strand Bias\"");
 
+        // FORMAT fields if not in POOLED mode
         if ( UAC.genotypeModel != GenotypeCalculationModel.Model.POOLED )
             headerInfo.addAll(VCFGenotypeRecord.getSupportedHeaderStrings());
 
-        // TODO -- clean this up
+        // all of the arguments from the argument collection
-        headerInfo.add("UG_genotype_model=" + UAC.genotypeModel);
+        Field[] fields = UAC.getClass().getFields();
-        headerInfo.add("UG_base_model=" + UAC.baseModel);
+        for ( Field field: fields ) {
-        headerInfo.add("UG_heterozygosity=" + UAC.heterozygosity);
+            ArgumentTypeDescriptor atd = ArgumentTypeDescriptor.create(field.getType());
-        headerInfo.add("UG_genotype_mode=" + UAC.GENOTYPE);
+            List<ArgumentDefinition> adList = atd.createArgumentDefinitions(new ArgumentSource(field.getType(), field));
-        headerInfo.add("UG_all_bases_mode=" + UAC.ALL_BASES);
+            for ( ArgumentDefinition ad : adList )
-        headerInfo.add("UG_min_confidence=" + UAC.CONFIDENCE_THRESHOLD);
+                headerInfo.add("UG_" + ad.fullName + "=" + JVMUtils.getFieldValue(field, UAC));
-        headerInfo.add("UG_max_deletion_fraction=" + UAC.MAX_DELETION_FRACTION);
+        }
-        headerInfo.add("UG_max_coverage=" + UAC.MAX_READS_IN_PILEUP);
-        if ( UAC.POOLSIZE > 0 )
-            headerInfo.add("UG_poolSize=" + UAC.POOLSIZE);
-        if ( UAC.ASSUME_SINGLE_SAMPLE != null )
-            headerInfo.add("UG_single_sample=" + UAC.ASSUME_SINGLE_SAMPLE);
-        if ( UAC.defaultPlatform != null )
-            headerInfo.add("UG_default_platform=" + UAC.defaultPlatform);
 
         return headerInfo;
     }

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -47,7 +47,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot1PointEM() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("c7aec953aac01101f0556db166178590"));
+                Arrays.asList("12d07018d9604b86b854e0c9132b0608"));
         executeTest("testMultiSamplePilot1 - Point Estimate EM", spec);
     }
 
@@ -55,7 +55,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot2PointEM() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("e03b5ac5821dc0e0da3cc8a1f686ec6b"));
+                Arrays.asList("65a808f077447f89e001e1cce8433acc"));
         executeTest("testMultiSamplePilot2 - Point Estimate EM", spec);
     }
 
@@ -68,7 +68,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testPooled1() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,000-10,024,000 -bm empirical -gm POOLED -ps 60 -confidence 30", 1,
-                Arrays.asList("d7579207d2521f36648b2b43be805bc4"));
+                Arrays.asList("4890ce37667379a0b60892cb0b9d8e09"));
         executeTest("testPooled1", spec);
     }
 
@@ -81,7 +81,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot1Joint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("d1076029884939017817061cfd06d8ff"));
+                Arrays.asList("fd5291c7115a558a7a6309ab417d2d57"));
         executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
     }
 
@@ -89,7 +89,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot2Joint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("58422eb06214282fc6e9efbf52937e1e"));
+                Arrays.asList("58ddc9426a25d0c3604af8da4eaa8294"));
         executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
     }
 
@@ -97,7 +97,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testSingleSamplePilot2Joint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("27fadaf914ad7fbc83d4f8367f43bc40"));
+                Arrays.asList("52e7030fe0968cd1a9b95154d8056b3f"));
         executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
     }
 
@@ -105,7 +105,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testGenotypeModeJoint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -genotype -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,001,000 -bm empirical -gm JOINT_ESTIMATE -confidence 70", 1,
-                Arrays.asList("6971e0bfa524c0e006b3c3ccef52520a"));
+                Arrays.asList("1ac9c9c8be0eb6adee7c67fac7c19c0d"));
         executeTest("testGenotypeMode - Joint Estimate", spec);
     }
 
@@ -113,7 +113,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testAllBasesModeJoint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -all_bases -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,001,000 -bm empirical -gm JOINT_ESTIMATE -confidence 70", 1,
-                Arrays.asList("9f54482c1594bdd1e28b4cf2e51f944f"));
+                Arrays.asList("37177e194a602749d31e5ecbf80ad309"));
         executeTest("testAllBasesMode - Joint Estimate", spec);
     }