zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Yet more argument consistency updates 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4089 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-23 20:52:30 +00:00
parent 3aedd0055e
commit ef795825fd
10 changed files with 50 additions and 86 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

19
java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
View File

@ -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) {
if ( vcfwriter != null )
vcfwriter.close();
}
public void onTraversalDone(Integer sum) {}
}

8
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
View File

@ -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);
}

14
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
View File

@ -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.close();
vcfwriter.add(record.first, record.second);
vcfwriter.close();
}

13
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
View File

@ -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) {
if ( vcfWriter != null )
vcfWriter.close();
}
public void onTraversalDone(Integer sum) {}
}

9
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
View File

@ -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.");
}
}

11
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
View File

@ -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.");
}
}

11
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -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");

9
java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java
View File

@ -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);
}

18
java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
View File

@ -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
private PrintStream out;
@Output(doc="File to which variants should be written",required=true)
protected VCFWriter vcfWriter = null;
@Argument(fullName="output_file", shortName="output", doc="VCF file to which output should be written", required=true)
private String OUTPUT_FILE = null;
@Argument(fullName="output_file", shortName="output", doc="Please use --out instead")
@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);
vcfWriter.close();
System.out.printf("Processed %d loci.\n", result);
}
}

24
java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java
View File

@ -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());
out.println("Number of variant sites observed: " + result.getNumVarSites());
out.println("Average coverage: " + ((double) result.getNumReads() / result.getNumVarSites()));
System.out.println("Number of reads observed: " + result.getNumReads());
System.out.println("Number of variant sites observed: " + 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) {