Yet more argument consistency updates

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4089 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java

@@ -42,7 +42,6 @@ import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 
 import java.util.*;
-import java.io.PrintStream;
 
 /**
  * Converts variants from other file formats to VCF format.
@@ -50,17 +49,17 @@ import java.io.PrintStream;
 @Requires(value={},referenceMetaData=@RMD(name=VariantsToVCF.INPUT_ROD_NAME, type=VariantContext.class))
 @Reference(window=@Window(start=0,stop=40))
 public class VariantsToVCF extends RodWalker<Integer, Integer> {
-    @Output
+
-    private PrintStream out;
+    @Output(doc="File to which variants should be written",required=true)
+    protected VCFWriter vcfwriter = null;
 
     public static final String INPUT_ROD_NAME = "variant";
 
     @Argument(fullName="sample", shortName="sample", doc="The sample name represented by the variant rod (for data like GELI with genotypes)", required=false)
     protected String sampleName = null;
 
-    private VCFWriter vcfwriter = null;
-
     private Set<String> allowedGenotypeFormatStrings = new HashSet<String>();
+    private boolean wroteHeader = false;
 
     // Don't allow mixed types for now
     private EnumSet<VariantContext.Type> ALLOWED_VARIANT_CONTEXT_TYPES = EnumSet.of(VariantContext.Type.SNP,
@@ -95,7 +94,9 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
     }
 
     private void writeRecord(VariantContext vc, RefMetaDataTracker tracker, byte ref) {
-        if ( vcfwriter == null ) {
+        if ( !wroteHeader ) {
+            wroteHeader = true;
+
             // setup the header fields
             Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
             hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
@@ -129,7 +130,6 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
                 }
             }
 
-            vcfwriter = new StandardVCFWriter(out);
             vcfwriter.writeHeader(new VCFHeader(hInfo, samples));
         }
 
@@ -145,8 +145,5 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
         return value + sum;
     }
 
-    public void onTraversalDone(Integer sum) {
+    public void onTraversalDone(Integer sum) {}
-        if ( vcfwriter != null )
-            vcfwriter.close();
-    }
 }

java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java

@@ -50,7 +50,7 @@ import java.util.*;
 @Reference(window=@Window(start=-50,stop=50))
 public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
 
-    @Output(doc="File to which variants should be written",required=true)
+    @Output(doc="File to which variants should be written",required=false)
     protected VCFWriter writer = null;
 
     @Argument(fullName="filterExpression", shortName="filter", doc="One or more expression used with INFO fields to filter (see wiki docs for more info)", required=false)
@@ -85,7 +85,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
     private FiltrationContextWindow variantContextWindow;
     private static final int windowSize = 10;  // 10 variants on either end of the current one
     private ArrayList<FiltrationContext> windowInitializer = new ArrayList<FiltrationContext>();
-
+    private boolean wroteHeader = false;
 
     private void initializeVcfWriter(VariantContext vc) {
         // setup the header fields
@@ -220,8 +220,10 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
     }
 
     private void writeVCF(VariantContext vc, byte ref) {
-        if ( writer == null )
+        if ( !wroteHeader ) {
             initializeVcfWriter(vc);
+            wroteHeader = true;
+        }
         writer.add(vc, ref);
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java

@@ -42,7 +42,6 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 
 import java.util.*;
-import java.io.PrintStream;
 
 /**
  * Converts Sequenom files to a VCF annotated with QC metrics (HW-equilibrium, % failed probes)
@@ -50,8 +49,9 @@ import java.io.PrintStream;
 @Reference(window=@Window(start=0,stop=40))
 @Requires(value={},referenceMetaData=@RMD(name="sequenom",type= Feature.class))
 public class SequenomValidationConverter extends RodWalker<Pair<VariantContext, Byte>,Integer> {
-    @Output
+
-    protected PrintStream out;
+    @Output(doc="File to which variants should be written",required=true)
+    protected VCFWriter vcfwriter = null;
 
     @Argument(fullName="maxHardy", doc="Maximum phred-scaled Hardy-Weinberg violation pvalue to consider an assay valid [default:20]", required=false)
     protected double maxHardy = 20.0;
@@ -122,8 +122,6 @@ public class SequenomValidationConverter extends RodWalker<Pair<VariantContext,
         if ( sampleNames == null )
             sampleNames = new TreeSet<String>();
 
-        VCFWriter vcfWriter = new StandardVCFWriter(out);
-
         // set up the info and filter headers
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
         hInfo.add(new VCFHeaderLine("source", "SequenomValidationConverter"));
@@ -161,11 +159,11 @@ public class SequenomValidationConverter extends RodWalker<Pair<VariantContext,
         }
         
         VCFHeader header = new VCFHeader(hInfo, sampleNames);
-        vcfWriter.writeHeader(header);
+        vcfwriter.writeHeader(header);
 
         for ( Pair<VariantContext, Byte> record : records )
-            vcfWriter.add(record.first, record.second);
+            vcfwriter.add(record.first, record.second);
-        vcfWriter.close();
+        vcfwriter.close();
     }
 
 

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

@@ -43,7 +43,6 @@ import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 
 import java.util.*;
-import java.io.PrintStream;
 
 /**
  * Combines VCF records from different sources; supports both full merges and set unions.
@@ -54,8 +53,9 @@ import java.io.PrintStream;
 @Reference(window=@Window(start=-50,stop=50))
 @Requires(value={})
 public class CombineVariants extends RodWalker<Integer, Integer> {
-    @Output
+
-    private PrintStream out;
+    @Output(doc="File to which variants should be written",required=true)
+    protected VCFWriter vcfWriter = null;
 
     // the types of combinations we currently allow
     @Argument(shortName="genotypeMergeOptions", doc="How should we merge genotype records for samples shared across the ROD files?", required=false)
@@ -79,13 +79,11 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
     @Argument(fullName="setKey", shortName="setKey", doc="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from.  Set to null if you don't want the set field emitted.", required=false)
     public String SET_KEY = "set";
 
-    private VCFWriter vcfWriter = null;
     private List<String> priority = null;
 
     private VariantAnnotatorEngine engine;
 
     public void initialize() {
-        vcfWriter = new StandardVCFWriter(out);
         validateAnnotateUnionArguments();
 
         Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), null);
@@ -154,8 +152,5 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
         return counter + sum;
     }
 
-    public void onTraversalDone(Integer sum) {
+    public void onTraversalDone(Integer sum) {}
-        if ( vcfWriter != null )
-            vcfWriter.close();
-    }
 }

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

@@ -25,7 +25,6 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.StandardVCFWriter;
 import org.broad.tribble.vcf.VCFWriter;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
@@ -37,17 +36,15 @@ import org.broadinstitute.sting.commandline.Output;
 import org.broad.tribble.vcf.VCFHeader;
 
 import java.util.*;
-import java.io.PrintStream;
 
 /**
  * Filters a lifted-over VCF file for ref bases that have been changed.
  */
 @Requires(value={},referenceMetaData=@RMD(name="variant",type= VariantContext.class))
 public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
-    @Output
-    PrintStream out;
 
-    private VCFWriter writer;
+    @Output(doc="File to which variants should be written",required=true)
+    protected VCFWriter writer = null;
 
     private long failedLocs = 0, totalLocs = 0;
 
@@ -55,7 +52,6 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
         Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList("variant"));
         Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList("variant"));
 
-        writer = new StandardVCFWriter(out);
         final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey("variant") ? vcfHeaders.get("variant").getMetaData() : null, samples);
         writer.writeHeader(vcfHeader);
     }
@@ -89,7 +85,6 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
     public Integer reduce(Integer value, Integer sum) { return 0; }
 
     public void onTraversalDone(Integer result) {
-        writer.close();
         System.out.println("Filtered " + failedLocs + " records out of " + totalLocs + " total records.");
     }
 }

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

@@ -25,7 +25,6 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.StandardVCFWriter;
 import org.broad.tribble.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
@@ -40,7 +39,6 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils
 import org.broad.tribble.vcf.VCFHeader;
 
 import java.io.File;
-import java.io.PrintStream;
 import java.util.*;
 
 import net.sf.picard.liftover.LiftOver;
@@ -53,8 +51,9 @@ import net.sf.samtools.SAMFileReader;
  */
 @Requires(value={},referenceMetaData=@RMD(name="variant", type=VariantContext.class))
 public class LiftoverVariants extends RodWalker<Integer, Integer> {
-    @Output
+
-    protected PrintStream out;
+    @Output(doc="File to which variants should be written",required=true)
+    protected VCFWriter writer = null;
 
     @Argument(fullName="chain", shortName="chain", doc="Chain file", required=true)
     protected File CHAIN = null;
@@ -62,8 +61,6 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
     @Argument(fullName="newSequenceDictionary", shortName="dict", doc="Sequence .dict file for the new build", required=true)
     protected File NEW_SEQ_DICT = null;
 
-    private VCFWriter writer;
-
     private LiftOver liftOver;
 
     private long successfulIntervals = 0, failedIntervals = 0;
@@ -78,7 +75,6 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
         Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList("variant"));
         Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList("variant"));
 
-        writer = new StandardVCFWriter(out);
         final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey("variant") ? vcfHeaders.get("variant").getMetaData() : null, samples);
         writer.writeHeader(vcfHeader);
     }
@@ -113,7 +109,6 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
     public Integer reduce(Integer value, Integer sum) { return 0; }
 
     public void onTraversalDone(Integer result) {
-        writer.close();
         System.out.println("Converted " + successfulIntervals + " records; failed to convert " + failedIntervals + " records.");
     }
 }

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

@@ -26,7 +26,6 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.StandardVCFWriter;
 import org.broad.tribble.vcf.VCFHeader;
 import org.broad.tribble.vcf.VCFHeaderLine;
 import org.broad.tribble.vcf.VCFWriter;
@@ -46,7 +45,6 @@ import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
-import java.io.PrintStream;
 import java.io.File;
 import java.io.FileNotFoundException;
 
@@ -56,8 +54,9 @@ import java.io.FileNotFoundException;
  */
 @Requires(value={},referenceMetaData=@RMD(name="variant", type=VariantContext.class))
 public class SelectVariants extends RodWalker<Integer, Integer> {
-    @Output
+
-    private PrintStream out;
+    @Output(doc="File to which variants should be written",required=true)
+    protected VCFWriter vcfWriter = null;
 
     @Argument(fullName="sample", shortName="sn", doc="Sample(s) to include.  Can be a single sample, specified multiple times for many samples, a file containing sample names, a regular expression to select many samples, or any combination thereof.", required=false)
     public Set<String> SAMPLE_EXPRESSIONS;
@@ -78,14 +77,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
     private Set<String> possibleSampleRegexs = new HashSet<String>();
     private Set<String> sampleExpressionsThatDidNotWork = new HashSet<String>();
 
-    private VCFWriter vcfWriter = null;
-
     /**
      * Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher
      */
     public void initialize() {
-        vcfWriter = new StandardVCFWriter(out);
-
         ArrayList<String> rodNames = new ArrayList<String>();
         rodNames.add("variant");
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java

@@ -21,7 +21,6 @@ import org.broadinstitute.sting.utils.vcf.VCFUtils;
 
 import java.io.File;
 import java.io.IOException;
-import java.io.PrintStream;
 import java.util.*;
 
 /**
@@ -31,8 +30,10 @@ import java.util.*;
  * @Date Apr 21, 2010
  */
 public class IndelAnnotator extends RodWalker<Integer,Long>{
-    @Output
+
-    PrintStream out;
+    @Output(doc="File to which variants should be written",required=true)
+    protected VCFWriter vcfWriter = null;
+
     @Argument(fullName="refseq", shortName="refseq",
 			doc="Name of RefSeq transcript annotation file. If specified, indels will be annotated with GENOMIC/UTR/INTRON/CODING and with the gene name", required=true)
 	String RefseqFileName = null;
@@ -44,7 +45,6 @@ public class IndelAnnotator extends RodWalker<Integer,Long>{
     private static String annUnknown = "UNKNOWN";
 
     private SeekableRODIterator refseqIterator;
-    private VCFWriter vcfWriter;
 
     private String getAnnotationString(RODRecordList ann) {
         if ( ann == null ) return annGenomic;
@@ -88,7 +88,6 @@ public class IndelAnnotator extends RodWalker<Integer,Long>{
         anno.add(new VCFInfoHeaderLine("type",1, VCFHeaderLineType.String,"Genomic interpretation (according to RefSeq)"));
         hInfo.addAll(anno);
 
-        vcfWriter = new StandardVCFWriter(out);
         VCFHeader vcfHeader = new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit()));
         vcfWriter.writeHeader(vcfHeader);
     }

java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java

@@ -45,7 +45,6 @@ import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broad.tribble.vcf.*;
 
-import java.io.*;
 import java.util.*;
 import static java.lang.Math.log10;
 
@@ -63,20 +62,18 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
     public static final String PROBS_ROD_NAME = "beagleProbs";
     public static final String PHASED_ROD_NAME = "beaglePhased";
 
-    @Output
+    @Output(doc="File to which variants should be written",required=true)
-    private PrintStream out;
+    protected VCFWriter vcfWriter = null;
 
-    @Argument(fullName="output_file", shortName="output", doc="VCF file to which output should be written", required=true)
+    @Argument(fullName="output_file", shortName="output", doc="Please use --out instead")
-    private String OUTPUT_FILE = null;
+    @Deprecated
+    private String oldOutputArg;
 
     @Argument(fullName="no" +
             "call_threshold", shortName="ncthr", doc="Threshold of confidence at which a genotype won't be called", required=false)
     private double noCallThreshold = 0.0;
 
     protected static String line = null;
-    private VCFWriter vcfWriter;
-
-
 
     private final double MIN_PROB_ERROR = 0.000001;
     private final double MAX_GENOTYPE_QUALITY = 6.0;
@@ -94,7 +91,6 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
         hInfo.add(new VCFHeaderLine("source", "BeagleImputation"));
 
         // Open output file specified by output VCF ROD
-        vcfWriter = new StandardVCFWriter(new File(OUTPUT_FILE));
         final List<ReferenceOrderedDataSource> dataSources = this.getToolkit().getRodDataSources();
 
         for( final ReferenceOrderedDataSource source : dataSources ) {
@@ -354,8 +350,6 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
      * @param result  the number of loci seen.
      */
     public void onTraversalDone(Integer result) {
-        out.printf("Processed %d loci.\n", result);
+        System.out.printf("Processed %d loci.\n", result);
-
-        vcfWriter.close();
     }
 }

java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java

@@ -55,8 +55,9 @@ import java.util.*;
 @ReadFilters( {ZeroMappingQualityReadFilter.class} ) // Filter out all reads with zero mapping quality
 
 public class ReadBackedPhasingWalker extends LocusWalker<PhasingStatsAndOutput, PhasingStats> {
-    @Output
+
-    protected PrintStream out;
+    @Output(doc="File to which variants should be written",required=true)
+    protected VCFWriter writer = null;
 
     @Argument(fullName = "cacheWindowSize", shortName = "cacheWindow", doc = "The window size (in bases) to cache variant sites and their reads; [default:20000]", required = false)
     protected Integer cacheWindow = 20000;
@@ -67,13 +68,9 @@ public class ReadBackedPhasingWalker extends LocusWalker<PhasingStatsAndOutput,
     @Argument(fullName = "phaseQualityThresh", shortName = "phaseThresh", doc = "The minimum phasing quality score required to output phasing; [default:4.77]", required = false)
     protected Double phaseQualityThresh = 4.77; // PQ = 4.77 <=> P(error) = 10^(-4.77/10) = 0.33, P(correct) = 0.66, so that we have odds ratio of >= 2
 
-    @Argument(fullName = "phasedVCFFile", shortName = "phasedVCF", doc = "The name of the phased VCF file output", required = true)
-    protected String phasedVCFFile = null;
-
     @Argument(fullName = "variantStatsFilePrefix", shortName = "variantStats", doc = "The prefix of the VCF/phasing statistics files", required = false)
     protected String variantStatsFilePrefix = null;
 
-    private VCFWriter writer = null;
     private PhasingQualityStatsWriter statsWriter = null;
 
     private LinkedList<VariantAndReads> siteQueue = null;
@@ -90,7 +87,6 @@ public class ReadBackedPhasingWalker extends LocusWalker<PhasingStatsAndOutput,
         hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
         hInfo.add(new VCFFormatHeaderLine("PQ", 1, VCFHeaderLineType.Float, "Read-backed phasing quality"));
 
-        writer = new StandardVCFWriter(new File(phasedVCFFile));
         writer.writeHeader(new VCFHeader(hInfo, new TreeSet<String>(vc.getSampleNames())));
     }
 
@@ -404,21 +400,19 @@ public class ReadBackedPhasingWalker extends LocusWalker<PhasingStatsAndOutput,
     public void onTraversalDone(PhasingStats result) {
         List<VariantContext> finalList = processQueue(null, result);
         writeVarContList(finalList);
-        if (writer != null)
-            writer.close();
         if (statsWriter != null)
             statsWriter.close();
 
-        out.println("Number of reads observed: " + result.getNumReads());
+        System.out.println("Number of reads observed: " + result.getNumReads());
-        out.println("Number of variant sites observed: " + result.getNumVarSites());
+        System.out.println("Number of variant sites observed: " + result.getNumVarSites());
-        out.println("Average coverage: " + ((double) result.getNumReads() / result.getNumVarSites()));
+        System.out.println("Average coverage: " + ((double) result.getNumReads() / result.getNumVarSites()));
 
-        out.println("\n-- Phasing summary [minimal haplotype probability: " + phaseQualityThresh + "] --");
+        System.out.println("\n-- Phasing summary [minimal haplotype probability: " + phaseQualityThresh + "] --");
         for (Map.Entry<String, PhaseCounts> sampPhaseCountEntry : result.getPhaseCounts()) {
             PhaseCounts pc = sampPhaseCountEntry.getValue();
-            out.println("Sample: " + sampPhaseCountEntry.getKey() + "\tNumber of tested sites: " + pc.numTestedSites + "\tNumber of phased sites: " + pc.numPhased);
+            System.out.println("Sample: " + sampPhaseCountEntry.getKey() + "\tNumber of tested sites: " + pc.numTestedSites + "\tNumber of phased sites: " + pc.numPhased);
         }
-        out.println("");
+        System.out.println("");
     }
 
     protected void writeVarContList(List<VariantContext> varContList) {