+ * argument which sets how many unobserved counts to add to every bin. Use --smoothing 0 to turn off all smoothing or, for example,
+ * --smoothing 15 for a large amount of smoothing.
+ */
+ @Argument(fullName="smoothing", shortName="sm", required = false, doc="Number of imaginary counts to add to each bin in order to smooth out bins with few data points")
private int SMOOTHING = 1;
- @Argument(fullName="max_quality_score", shortName="maxQ", required = false, doc="The integer value at which to cap the quality scores, default=50")
+
+ /**
+ * Combinations of covariates in which there are zero mismatches technically have infinite quality. We get around this situation
+ * by capping at the specified value. We've found that Q40 is too low when using a more completely database of known variation like dbSNP build 132 or later.
+ */
+ @Argument(fullName="max_quality_score", shortName="maxQ", required = false, doc="The integer value at which to cap the quality scores")
private int MAX_QUALITY_SCORE = 50;
+
+ /**
+ * By default TableRecalibration emits the OQ field -- so you can go back and look at the original quality scores, rerun
+ * the system using the OQ flags, etc, on the output BAM files; to turn off emission of the OQ field use this flag.
+ */
@Argument(fullName="doNotWriteOriginalQuals", shortName="noOQs", required=false, doc="If true, we will not write the original quality (OQ) tag for each read")
private boolean DO_NOT_WRITE_OQ = false;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
new file mode 100755
index 000000000..fc23200af
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
@@ -0,0 +1,438 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.validation;
+
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Input;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.commandline.RodBinding;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
+import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
+import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
+import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
+import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.MutableVariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+
+import java.util.Map;
+import java.util.Set;
+
+import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
+
+/**
+ * Genotypes a dataset and validates the calls of another dataset using the Unified Genotyper.
+ *
+ *
+ * Genotype and Validate is a tool to evaluate the quality of a dataset for calling SNPs
+ * and Indels given a secondary (validation) data source. The data sources are BAM or VCF
+ * files. You can use them interchangeably (i.e. a BAM to validate calls in a VCF or a VCF
+ * to validate calls on a BAM).
+ *
+ *
+ *
+ * The simplest scenario is when you have a VCF of hand annotated SNPs and Indels, and you
+ * want to know how well a particular technology performs calling these snps. With a
+ * dataset (BAM file) generated by the technology in test, and the hand annotated VCF, you
+ * can run GenotypeAndValidate to asses the accuracy of the calls with the new technology's
+ * dataset.
+ *
+ *
+ *
+ * Another option is to validate the calls on a VCF file, using a deep coverage BAM file
+ * that you trust the calls on. The GenotypeAndValidate walker will make calls using the
+ * reads in the BAM file and take them as truth, then compare to the calls in the VCF file
+ * and produce a truth table.
+ *
+ *
+ *
+ * Input
+ *
+ * A BAM file to make calls on and a VCF file to use as truth validation dataset.
+ *
+ * You also have the option to invert the roles of the files using the command line options listed below.
+ *
+ *
+ * Output
+ *
+ * GenotypeAndValidate has two outputs. The truth table and the optional VCF file. The truth table is a
+ * 2x2 table correlating what was called in the dataset with the truth of the call (whether it's a true
+ * positive or a false positive). The table should look like this:
+ *
+ *
+ *
+ *
+ * |
+ * ALT |
+ * REF |
+ * Predictive Value |
+ *
+ *
+ * | called alt |
+ * True Positive (TP) |
+ * False Positive (FP) |
+ * Positive PV |
+ *
+ *
+ * | called ref |
+ * False Negative (FN) |
+ * True Negative (TN) |
+ * Negative PV |
+ *
+ *
+ *
+ *
+ *
+ * The positive predictive value (PPV) is the proportion of subjects with positive test results
+ * who are correctly diagnosed.
+ *
+ *
+ * The negative predictive value (NPV) is the proportion of subjects with a negative test result
+ * who are correctly diagnosed.
+ *
+ *
+ * The VCF file will contain only the variants that were called or not called, excluding the ones that
+ * were uncovered or didn't pass the filters. This file is useful if you are trying to compare
+ * the PPV and NPV of two different technologies on the exact same sites (so you can compare apples to
+ * apples).
+ *
+ *
+ *
+ * Here is an example of an annotated VCF file (info field clipped for clarity)
+ *
+ *
+ * #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
+ * 1 20568807 . C T 0 HapMapHet AC=1;AF=0.50;AN=2;DP=0;GV=T GT 0/1
+ * 1 22359922 . T C 282 WG-CG-HiSeq AC=2;AF=0.50;GV=T;AN=4;DP=42 GT:AD:DP:GL:GQ 1/0 ./. 0/1:20,22:39:-72.79,-11.75,-67.94:99 ./.
+ * 13 102391461 . G A 341 Indel;SnpCluster AC=1;GV=F;AF=0.50;AN=2;DP=45 GT:AD:DP:GL:GQ ./. ./. 0/1:32,13:45:-50.99,-13.56,-112.17:99 ./.
+ * 1 175516757 . C G 655 SnpCluster,WG AC=1;AF=0.50;AN=2;GV=F;DP=74 GT:AD:DP:GL:GQ ./. ./. 0/1:52,22:67:-89.02,-20.20,-191.27:99 ./.
+ *
+ *
+ *
+ *
+ * Additional Details
+ *
+ * -
+ * You should always use -BTI on your VCF track, so that the GATK only looks at the sites on the VCF file.
+ * This speeds up the process a lot.
+ *
+ * -
+ * The total number of visited bases may be greater than the number of variants in the original
+ * VCF file because of extended indels, as they trigger one call per new insertion or deletion.
+ * (i.e. ACTG/- will count as 4 genotyper calls, but it's only one line in the VCF).
+ *
+ *
+ *
+ * Examples
+ *
+ * -
+ * Genotypes BAM file from new technology using the VCF as a truth dataset:
+ *
+ *
+ *
+ * java
+ * -jar /GenomeAnalysisTK.jar
+ * -T GenotypeAndValidate
+ * -R human_g1k_v37.fasta
+ * -I myNewTechReads.bam
+ * -alleles handAnnotatedVCF.vcf
+ * -BTI alleles
+ *
+ *
+ * -
+ * Using a BAM file as the truth dataset:
+ *
+ *
+ *
+ * java
+ * -jar /GenomeAnalysisTK.jar
+ * -T GenotypeAndValidate
+ * -R human_g1k_v37.fasta
+ * -I myTruthDataset.bam
+ * -alleles callsToValidate.vcf
+ * -BTI alleles
+ * -bt
+ * -o gav.vcf
+ *
+ *
+ *
+ * @author Mauricio Carneiro
+ * @since ${DATE}
+ */
+
+@Requires(value={DataSource.READS, DataSource.REFERENCE})
+@Allows(value={DataSource.READS, DataSource.REFERENCE})
+
+@By(DataSource.REFERENCE)
+@Reference(window=@Window(start=-200,stop=200))
+
+
+public class GenotypeAndValidateWalker extends RodWalker implements TreeReducible {
+
+ @Output(doc="Generate a VCF file with the variants considered by the walker, with a new annotation \"callStatus\" which will carry the value called in the validation VCF or BAM file", required=false)
+ protected VCFWriter vcfWriter = null;
+
+ @Input(fullName="alleles", shortName = "alleles", doc="The set of alleles at which to genotype", required=true)
+ public RodBinding alleles;
+
+ @Argument(fullName ="set_bam_truth", shortName ="bt", doc="Use the calls on the reads (bam file) as the truth dataset and validate the calls on the VCF", required=false)
+ private boolean bamIsTruth = false;
+
+ @Argument(fullName="minimum_base_quality_score", shortName="mbq", doc="Minimum base quality score for calling a genotype", required=false)
+ private int mbq = -1;
+
+ @Argument(fullName="maximum_deletion_fraction", shortName="deletions", doc="Maximum deletion fraction for calling a genotype", required=false)
+ private double deletions = -1;
+
+ @Argument(fullName="standard_min_confidence_threshold_for_calling", shortName="stand_call_conf", doc="the minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls", required=false)
+ private double callConf = -1;
+
+ @Argument(fullName="standard_min_confidence_threshold_for_emitting", shortName="stand_emit_conf", doc="the minimum phred-scaled Qscore threshold to emit low confidence calls", required=false)
+ private double emitConf = -1;
+
+ @Argument(fullName="condition_on_depth", shortName="depth", doc="Condition validation on a minimum depth of coverage by the reads", required=false)
+ private int minDepth = -1;
+
+ @Argument(fullName ="sample", shortName ="sn", doc="Name of the sample to validate (in case your VCF/BAM has more than one sample)", required=false)
+ private String sample = "";
+
+ private UnifiedGenotyperEngine snpEngine;
+ private UnifiedGenotyperEngine indelEngine;
+
+ public static class CountedData {
+ private long nAltCalledAlt = 0L;
+ private long nAltCalledRef = 0L;
+ private long nRefCalledAlt = 0L;
+ private long nRefCalledRef = 0L;
+ private long nNotConfidentCalls = 0L;
+ private long nUncovered = 0L;
+
+ /**
+ * Adds the values of other to this, returning this
+ * @param other the other object
+ */
+ public void add(CountedData other) {
+ nAltCalledAlt += other.nAltCalledAlt;
+ nAltCalledRef += other.nAltCalledRef;
+ nRefCalledAlt += other.nRefCalledAlt;
+ nRefCalledRef += other.nRefCalledRef;
+ nUncovered += other.nUncovered;
+ nNotConfidentCalls += other.nNotConfidentCalls;
+ }
+ }
+
+
+
+ //---------------------------------------------------------------------------------------------------------------
+ //
+ // initialize
+ //
+ //---------------------------------------------------------------------------------------------------------------
+
+ public void initialize() {
+
+ // Initialize VCF header
+ if (vcfWriter != null) {
+ Map header = VCFUtils.getVCFHeadersFromRodPrefix(getToolkit(), alleles.getName());
+ Set samples = SampleUtils.getSampleList(header, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
+ Set headerLines = VCFUtils.smartMergeHeaders(header.values(), logger);
+ headerLines.add(new VCFHeaderLine("source", "GenotypeAndValidate"));
+ vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
+ }
+
+ // Filling in SNP calling arguments for UG
+ UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
+ uac.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
+ uac.alleles = alleles;
+ if (!bamIsTruth) uac.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
+ if (mbq >= 0) uac.MIN_BASE_QUALTY_SCORE = mbq;
+ if (deletions >= 0) uac.MAX_DELETION_FRACTION = deletions;
+ if (emitConf >= 0) uac.STANDARD_CONFIDENCE_FOR_EMITTING = emitConf;
+ if (callConf >= 0) uac.STANDARD_CONFIDENCE_FOR_CALLING = callConf;
+
+ uac.GLmodel = GenotypeLikelihoodsCalculationModel.Model.SNP;
+ snpEngine = new UnifiedGenotyperEngine(getToolkit(), uac);
+
+ // Adding the INDEL calling arguments for UG
+ uac.GLmodel = GenotypeLikelihoodsCalculationModel.Model.INDEL;
+ indelEngine = new UnifiedGenotyperEngine(getToolkit(), uac);
+
+ // make sure we have callConf set to the threshold set by the UAC so we can use it later.
+ callConf = uac.STANDARD_CONFIDENCE_FOR_CALLING;
+ }
+
+ //---------------------------------------------------------------------------------------------------------------
+ //
+ // map
+ //
+ //---------------------------------------------------------------------------------------------------------------
+
+ public CountedData map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
+
+ final CountedData counter = new CountedData();
+
+ // For some reason RodWalkers get map calls with null trackers
+ if( tracker == null )
+ return counter;
+
+ VariantContext vcComp = tracker.getFirstValue(alleles);
+ if( vcComp == null )
+ return counter;
+
+ //todo - not sure I want this, may be misleading to filter extended indel events.
+ if (isInsideExtendedIndel(vcComp, ref))
+ return counter;
+
+ // Do not operate on variants that are not covered to the optional minimum depth
+ if (!context.hasReads() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
+ counter.nUncovered = 1L;
+ return counter;
+ }
+
+ VariantCallContext call;
+ if ( vcComp.isSNP() )
+ call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
+ else if ( vcComp.isIndel() ) {
+ call = indelEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
+ }
+ else {
+ logger.info("Not SNP or INDEL " + vcComp.getChr() + ":" + vcComp.getStart() + " " + vcComp.getAlleles());
+ return counter;
+ }
+
+
+ boolean writeVariant = true;
+
+ if (bamIsTruth) {
+ if (call.confidentlyCalled) {
+ // If truth is a confident REF call
+ if (call.isVariant()) {
+ if (vcComp.isVariant())
+ counter.nAltCalledAlt = 1L; // todo -- may wanna check if the alts called are the same?
+ else
+ counter.nAltCalledRef = 1L;
+ }
+ // If truth is a confident ALT call
+ else {
+ if (vcComp.isVariant())
+ counter.nRefCalledAlt = 1L;
+ else
+ counter.nRefCalledRef = 1L;
+ }
+ }
+ else {
+ counter.nNotConfidentCalls = 1L;
+ writeVariant = false;
+ }
+ }
+ else {
+ if (!vcComp.hasAttribute("GV"))
+ throw new UserException.BadInput("Variant has no GV annotation in the INFO field. " + vcComp.getChr() + ":" + vcComp.getStart());
+
+
+
+ if (call.isCalledAlt(callConf)) {
+ if (vcComp.getAttribute("GV").equals("T"))
+ counter.nAltCalledAlt = 1L;
+ else
+ counter.nRefCalledAlt = 1L;
+ }
+ else if (call.isCalledRef(callConf)) {
+ if (vcComp.getAttribute("GV").equals("T"))
+ counter.nAltCalledRef = 1L;
+ else
+ counter.nRefCalledRef = 1L;
+ }
+ else {
+ counter.nNotConfidentCalls = 1L;
+ writeVariant = false;
+ }
+ }
+
+ if (vcfWriter != null && writeVariant) {
+ if (!vcComp.hasAttribute("callStatus")) {
+ MutableVariantContext mvc = new MutableVariantContext(vcComp);
+ mvc.putAttribute("callStatus", call.isCalledAlt(callConf) ? "ALT" : "REF" );
+ vcfWriter.add(mvc);
+ }
+ else
+ vcfWriter.add(vcComp);
+ }
+ return counter;
+ }
+
+ //---------------------------------------------------------------------------------------------------------------
+ //
+ // reduce
+ //
+ //---------------------------------------------------------------------------------------------------------------
+
+ public CountedData reduceInit() {
+ return new CountedData();
+ }
+
+ public CountedData treeReduce( final CountedData sum1, final CountedData sum2) {
+ sum2.add(sum1);
+ return sum2;
+ }
+
+ public CountedData reduce( final CountedData mapValue, final CountedData reduceSum ) {
+ reduceSum.add(mapValue);
+ return reduceSum;
+ }
+
+ public void onTraversalDone( CountedData reduceSum ) {
+ double ppv = 100 * ((double) reduceSum.nAltCalledAlt /( reduceSum.nAltCalledAlt + reduceSum.nRefCalledAlt));
+ double npv = 100 * ((double) reduceSum.nRefCalledRef /( reduceSum.nRefCalledRef + reduceSum.nAltCalledRef));
+ double sensitivity = 100 * ((double) reduceSum.nAltCalledAlt /( reduceSum.nAltCalledAlt + reduceSum.nAltCalledRef));
+ double specificity = (reduceSum.nRefCalledRef + reduceSum.nRefCalledAlt > 0) ? 100 * ((double) reduceSum.nRefCalledRef /( reduceSum.nRefCalledRef + reduceSum.nRefCalledAlt)) : 100;
+ logger.info(String.format("Resulting Truth Table Output\n\n" +
+ "---------------------------------------------------\n" +
+ "\t\t|\tALT\t|\tREF\t\n" +
+ "---------------------------------------------------\n" +
+ "called alt\t|\t%d\t|\t%d\n" +
+ "called ref\t|\t%d\t|\t%d\n" +
+ "---------------------------------------------------\n" +
+ "positive predictive value: %f%%\n" +
+ "negative predictive value: %f%%\n" +
+ "---------------------------------------------------\n" +
+ "sensitivity: %f%%\n" +
+ "specificity: %f%%\n" +
+ "---------------------------------------------------\n" +
+ "not confident: %d\n" +
+ "not covered: %d\n" +
+ "---------------------------------------------------\n", reduceSum.nAltCalledAlt, reduceSum.nRefCalledAlt, reduceSum.nAltCalledRef, reduceSum.nRefCalledRef, ppv, npv, sensitivity, specificity, reduceSum.nNotConfidentCalls, reduceSum.nUncovered));
+ }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
index 7653f511f..61149e5d9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
@@ -14,9 +14,8 @@ import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
+import org.broadinstitute.sting.utils.codecs.table.TableFeature;
import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.BaseUtils;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index b52863c8f..f6b6a8d65 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -191,16 +191,28 @@ public class SelectVariants extends RodWalker {
protected VCFWriter vcfWriter = null;
@Argument(fullName="sample_name", shortName="sn", doc="Include genotypes from this sample. Can be specified multiple times", required=false)
- public Set sampleNames;
+ public Set sampleNames = new HashSet(0);
@Argument(fullName="sample_expressions", shortName="se", doc="Regular expression to select many samples from the ROD tracks provided. Can be specified multiple times", required=false)
- public Set sampleExpressions;
+ public Set sampleExpressions ;
@Argument(fullName="sample_file", shortName="sf", doc="File containing a list of samples (one per line) to include. Can be specified multiple times", required=false)
public Set sampleFiles;
/**
- * Note that thse expressions are evaluated *after* the specified samples are extracted and the INFO field annotations are updated.
+ * Note that sample exclusion takes precedence over inclusion, so that if a sample is in both lists it will be excluded.
+ */
+ @Argument(fullName="exclude_sample_name", shortName="xl_sn", doc="Exclude genotypes from this sample. Can be specified multiple times", required=false)
+ public Set XLsampleNames = new HashSet(0);
+
+ /**
+ * Note that sample exclusion takes precedence over inclusion, so that if a sample is in both lists it will be excluded.
+ */
+ @Argument(fullName="exclude_sample_file", shortName="xl_sf", doc="File containing a list of samples (one per line) to exclude. Can be specified multiple times", required=false)
+ public Set XLsampleFiles;
+
+ /**
+ * Note that these expressions are evaluated *after* the specified samples are extracted and the INFO field annotations are updated.
*/
@Argument(shortName="select", doc="One or more criteria to use when selecting the data", required=false)
public ArrayList SELECT_EXPRESSIONS = new ArrayList();
@@ -304,8 +316,7 @@ public class SelectVariants extends RodWalker {
private ArrayList afBoosts = null;
double bkDelta = 0.0;
-
- private PrintStream outMVFileStream = null;
+ private PrintStream outMVFileStream = null;
/**
@@ -321,19 +332,27 @@ public class SelectVariants extends RodWalker {
Collection samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFiles);
Collection samplesFromExpressions = SampleUtils.matchSamplesExpressions(vcfSamples, sampleExpressions);
+ // first, add any requested samples
samples.addAll(samplesFromFile);
samples.addAll(samplesFromExpressions);
- if (sampleNames != null)
- samples.addAll(sampleNames);
+ samples.addAll(sampleNames);
- if(samples.isEmpty()) {
+ // if none were requested, we want all of them
+ if ( samples.isEmpty() ) {
samples.addAll(vcfSamples);
NO_SAMPLES_SPECIFIED = true;
}
- for (String sample : samples) {
+ // now, exclude any requested samples
+ Collection XLsamplesFromFile = SampleUtils.getSamplesFromFiles(XLsampleFiles);
+ samples.removeAll(XLsamplesFromFile);
+ samples.removeAll(XLsampleNames);
+
+ if ( samples.size() == 0 )
+ throw new UserException("All samples requested to be included were also requested to be excluded.");
+
+ for ( String sample : samples )
logger.info("Including sample '" + sample + "'");
- }
// Initialize VCF header
Set headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), logger);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
index 61851abe2..12e62a249 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
@@ -33,7 +33,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
-import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.*;
@@ -120,7 +119,7 @@ public class VariantsToVCF extends RodWalker {
if ( tracker == null || !BaseUtils.isRegularBase(ref.getBase()) )
return 0;
- String rsID = dbsnp == null ? null : DbSNPHelper.rsIDOfFirstRealVariant(tracker.getValues(dbsnp.dbsnp, context.getLocation()), VariantContext.Type.SNP);
+ String rsID = dbsnp == null ? null : VCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbsnp.dbsnp, context.getLocation()), VariantContext.Type.SNP);
Collection contexts = getVariantContexts(tracker, ref);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java
rename to public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
index 5e536d4c1..e328c9286 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.refdata.features.beagle;
+package org.broadinstitute.sting.utils.codecs.beagle;
/*
* Copyright (c) 2010 The Broad Institute
*
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java
rename to public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java
index e6832754d..0aa9ecba2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java
@@ -22,7 +22,7 @@
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
-package org.broadinstitute.sting.gatk.refdata.features.beagle;
+package org.broadinstitute.sting.utils.codecs.beagle;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.utils.variantcontext.Allele;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java
index fef6c4ea0..c30da828e 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java
@@ -117,7 +117,7 @@ public class CGVarCodec implements FeatureCodec {
return new VariantContext("CGI", array[3], start, end, alleles, VariantContext.NO_NEG_LOG_10PERROR, null, attrs);
}
- public Class getFeatureType() {
+ public Class getFeatureType() {
return VariantContext.class;
}
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java
index 90878dee7..535f607a1 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java
@@ -82,7 +82,7 @@ public class RawHapMapCodec implements FeatureCodec {
headerLine);
}
- public Class getFeatureType() {
+ public Class getFeatureType() {
return RawHapMapFeature.class;
}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
similarity index 96%
rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java
rename to public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
index cec40b5bd..391715c63 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
@@ -1,6 +1,5 @@
-package org.broadinstitute.sting.gatk.refdata.features.refseq;
+package org.broadinstitute.sting.utils.codecs.refseq;
-import org.apache.commons.io.filefilter.FalseFileFilter;
import org.broad.tribble.Feature;
import org.broad.tribble.TribbleException;
import org.broad.tribble.readers.LineReader;
@@ -104,7 +103,7 @@ public class RefSeqCodec implements ReferenceDependentFeatureCodec getFeatureType() {
return RefSeqFeature.class;
}
}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
rename to public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java
index a38d45428..c04ca8592 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.refdata.features.refseq;
+package org.broadinstitute.sting.utils.codecs.refseq;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/Transcript.java b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/Transcript.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/Transcript.java
rename to public/java/src/org/broadinstitute/sting/utils/codecs/refseq/Transcript.java
index d8bf12810..3e8a4fb34 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/Transcript.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/Transcript.java
@@ -1,53 +1,53 @@
-package org.broadinstitute.sting.gatk.refdata.features.refseq;
-
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.HasGenomeLocation;
-
-import java.util.List;
-
-/**
- * Created by IntelliJ IDEA.
- * User: asivache
- * Date: Sep 22, 2009
- * Time: 5:22:30 PM
- * To change this template use File | Settings | File Templates.
- */
-public interface Transcript extends HasGenomeLocation {
-
- /** Returns id of the transcript (RefSeq NM_* id) */
- public String getTranscriptId();
- /** Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively */
- public int getStrand();
- /** Returns transcript's full genomic interval (includes all exons with UTRs) */
- public GenomeLoc getLocation();
- /** Returns genomic interval of the coding sequence (does not include
- * UTRs, but still includes introns, since it's a single interval on the DNA)
- */
- public GenomeLoc getCodingLocation();
- /** Name of the gene this transcript corresponds to (typically NOT gene id such as Entrez etc,
- * but the implementation can decide otherwise)
- */
- public String getGeneName();
- /** Number of exons in this transcript */
- public int getNumExons();
- /** Genomic location of the n-th exon; expected to throw an exception (runtime) if n is out of bounds */
- public GenomeLoc getExonLocation(int n);
-
- /** Returns the list of all exons in this transcript, as genomic intervals */
- public List getExons();
-
- /** Returns true if the specified interval 'that' overlaps with the full genomic interval of this transcript */
- public boolean overlapsP (GenomeLoc that);
-
- /** Returns true if the specified interval 'that' overlaps with the coding genomic interval of this transcript.
- * NOTE: since "coding interval" is still a single genomic interval, it will not contain UTRs of the outermost exons,
- * but it will still contain introns and/or exons internal to this genomic locus that are not spliced into this transcript.
- * @see #overlapsExonP
- */
- public boolean overlapsCodingP (GenomeLoc that);
-
- /** Returns true if the specified interval 'that' overlaps with any of the exons actually spliced into this transcript */
- public boolean overlapsExonP (GenomeLoc that);
-
-
-}
+package org.broadinstitute.sting.utils.codecs.refseq;
+
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.HasGenomeLocation;
+
+import java.util.List;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: asivache
+ * Date: Sep 22, 2009
+ * Time: 5:22:30 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public interface Transcript extends HasGenomeLocation {
+
+ /** Returns id of the transcript (RefSeq NM_* id) */
+ public String getTranscriptId();
+ /** Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively */
+ public int getStrand();
+ /** Returns transcript's full genomic interval (includes all exons with UTRs) */
+ public GenomeLoc getLocation();
+ /** Returns genomic interval of the coding sequence (does not include
+ * UTRs, but still includes introns, since it's a single interval on the DNA)
+ */
+ public GenomeLoc getCodingLocation();
+ /** Name of the gene this transcript corresponds to (typically NOT gene id such as Entrez etc,
+ * but the implementation can decide otherwise)
+ */
+ public String getGeneName();
+ /** Number of exons in this transcript */
+ public int getNumExons();
+ /** Genomic location of the n-th exon; expected to throw an exception (runtime) if n is out of bounds */
+ public GenomeLoc getExonLocation(int n);
+
+ /** Returns the list of all exons in this transcript, as genomic intervals */
+ public List getExons();
+
+ /** Returns true if the specified interval 'that' overlaps with the full genomic interval of this transcript */
+ public boolean overlapsP (GenomeLoc that);
+
+ /** Returns true if the specified interval 'that' overlaps with the coding genomic interval of this transcript.
+ * NOTE: since "coding interval" is still a single genomic interval, it will not contain UTRs of the outermost exons,
+ * but it will still contain introns and/or exons internal to this genomic locus that are not spliced into this transcript.
+ * @see #overlapsExonP
+ */
+ public boolean overlapsCodingP (GenomeLoc that);
+
+ /** Returns true if the specified interval 'that' overlaps with any of the exons actually spliced into this transcript */
+ public boolean overlapsExonP (GenomeLoc that);
+
+
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java
rename to public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java
index 43e2c3ff5..f4048d37d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java
@@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
-package org.broadinstitute.sting.gatk.refdata.features.sampileup;
+package org.broadinstitute.sting.utils.codecs.sampileup;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
@@ -35,7 +35,7 @@ import java.util.ArrayList;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import static org.broadinstitute.sting.gatk.refdata.features.sampileup.SAMPileupFeature.VariantType;
+import static org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature.VariantType;
/**
* A Tribble encoder / decoder for SAM pileup data.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java b/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java
rename to public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java
index 378f26934..eb33243e3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java
@@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
-package org.broadinstitute.sting.gatk.refdata.features.sampileup;
+package org.broadinstitute.sting.utils.codecs.sampileup;
import net.sf.samtools.util.StringUtil;
import org.broad.tribble.Feature;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java
rename to public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java
index 039b8adde..f6861e585 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java
@@ -22,7 +22,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
-package org.broadinstitute.sting.gatk.refdata.features.samread;
+package org.broadinstitute.sting.utils.codecs.samread;
import net.sf.samtools.Cigar;
import net.sf.samtools.TextCigarCodec;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadFeature.java b/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadFeature.java
rename to public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java
index 7f12b2b2f..fc1bf89af 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadFeature.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java
@@ -22,7 +22,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
-package org.broadinstitute.sting.gatk.refdata.features.samread;
+package org.broadinstitute.sting.utils.codecs.samread;
import org.broad.tribble.Feature;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java
index eada8521f..b5efb49a7 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java
@@ -222,7 +222,7 @@ public class SnpEffCodec implements FeatureCodec, SelfScopingFeatureCodec {
return null;
}
- public Class getFeatureType() {
+ public Class getFeatureType() {
return SnpEffFeature.class;
}
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java
index e169dbdfc..284c43e90 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java
@@ -178,7 +178,7 @@ public class SoapSNPCodec implements FeatureCodec, NameAwareCodec {
/**
* @return VariantContext
*/
- public Class getFeatureType() {
+ public Class getFeatureType() {
return VariantContext.class;
}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java
similarity index 94%
rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java
rename to public/java/src/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java
index 745ccdd9f..6fe1907e3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.refdata.features.table;
+package org.broadinstitute.sting.utils.codecs.table;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
similarity index 96%
rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java
rename to public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
index ab1ac59d8..2ce7c679e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.refdata.features.table;
+package org.broadinstitute.sting.utils.codecs.table;
import org.broad.tribble.Feature;
import org.broad.tribble.readers.LineReader;
@@ -51,7 +51,7 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
}
@Override
- public Class getFeatureType() {
+ public Class getFeatureType() {
return TableFeature.class;
}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java
similarity index 96%
rename from public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java
rename to public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java
index ca73ee960..a85849f0b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.refdata.features.table;
+package org.broadinstitute.sting.utils.codecs.table;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.utils.GenomeLoc;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
index cb505c717..19f58ddaa 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
@@ -263,7 +263,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
*
* @return the type of record
*/
- public Class getFeatureType() {
+ public Class getFeatureType() {
return VariantContext.class;
}
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
index f43891e77..c0a04c81f 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
@@ -180,4 +180,19 @@ public class VCFUtils {
return new HashSet(map.values());
}
+
+ public static String rsIDOfFirstRealVariant(List VCs, VariantContext.Type type) {
+ if ( VCs == null )
+ return null;
+
+ String rsID = null;
+ for ( VariantContext vc : VCs ) {
+ if ( vc.getType() == type ) {
+ rsID = vc.getID();
+ break;
+ }
+ }
+
+ return rsID;
+ }
}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java
index ce03c8093..214a1716a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java
@@ -71,7 +71,7 @@ public abstract class DocumentedGATKFeatureHandler {
* @return
*/
public String getDestinationFilename(ClassDoc doc, Class clazz) {
- return GATKDocUtils.htmlFilenameForClass(clazz);
+ return HelpUtils.htmlFilenameForClass(clazz);
}
/**
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java
deleted file mode 100644
index 8efeecd7b..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.help;
-
-/**
- * @author depristo
- * @since 8/8/11
- */
-public class GATKDocUtils {
- private final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/";
- private final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/";
- private final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/";
-
- public static String htmlFilenameForClass(Class c) {
- return c.getName().replace(".", "_") + ".html";
- }
-
- public static String helpLinksToGATKDocs(Class c) {
- String classPath = htmlFilenameForClass(c);
- StringBuilder b = new StringBuilder();
- b.append("release version: ").append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath).append("\n");
- b.append("stable version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n");
- b.append("unstable version: ").append(URL_ROOT_FOR_UNSTABLE_GATKDOCS).append(classPath).append("\n");
- return b.toString();
- }
-}
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
index 4527c6afe..da4e7bdaf 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
@@ -32,6 +32,10 @@ import org.broadinstitute.sting.utils.classloader.JVMUtils;
import java.lang.reflect.Field;
public class HelpUtils {
+ public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/";
+ public final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/";
+ public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/";
+
protected static boolean implementsInterface(ProgramElementDoc classDoc, Class... interfaceClasses) {
for (Class interfaceClass : interfaceClasses)
if (assignableToClass(classDoc, interfaceClass, false))
@@ -74,4 +78,17 @@ public class HelpUtils {
String.format("%s.%s", containingPackage.name(), doc.name()) :
String.format("%s", doc.name());
}
+
+ public static String htmlFilenameForClass(Class c) {
+ return c.getName().replace(".", "_") + ".html";
+ }
+
+ public static String helpLinksToGATKDocs(Class c) {
+ String classPath = htmlFilenameForClass(c);
+ StringBuilder b = new StringBuilder();
+ b.append("release version: ").append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath).append("\n");
+ b.append("stable version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n");
+ b.append("unstable version: ").append(URL_ROOT_FOR_UNSTABLE_GATKDOCS).append(classPath).append("\n");
+ return b.toString();
+ }
}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index ca3399c78..dacc2d94a 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -1080,8 +1080,8 @@ public class VariantContext implements Feature { // to enable tribble intergrati
}
public void validateReferenceBases(Allele reference, Byte paddedRefBase) {
- // don't validate if we're an insertion
- if ( !reference.isNull() && !reference.basesMatch(getReference()) ) {
+ // don't validate if we're an insertion or complex event
+ if ( !reference.isNull() && getReference().length() == 1 && !reference.basesMatch(getReference()) ) {
throw new TribbleException.InternalCodecException(String.format("the REF allele is incorrect for the record at position %s:%d, %s vs. %s", getChr(), getStart(), reference.getBaseString(), getReference().getBaseString()));
}
diff --git a/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java b/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
index 79e9172dd..013a37a88 100755
--- a/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
@@ -26,7 +26,6 @@
package org.broadinstitute.sting.commandline;
import org.broad.tribble.Feature;
-import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.testng.Assert;
@@ -35,7 +34,6 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-import javax.script.Bindings;
import java.util.List;
import java.util.EnumSet;
/**
diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java
index f782580e2..85ae1e1f7 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java
@@ -10,7 +10,7 @@ import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
+import org.broadinstitute.sting.utils.codecs.table.TableFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java
index bd4f93d24..d45f6e667 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java
@@ -4,7 +4,7 @@ import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
+import org.broadinstitute.sting.utils.codecs.table.TableFeature;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java
index fbd30bc8a..1e39fd26f 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java
@@ -31,7 +31,7 @@ import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
+import org.broadinstitute.sting.utils.codecs.table.TableFeature;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GenomeLoc;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java
index 5d662ffed..90262b9c1 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java
@@ -29,8 +29,8 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.refdata.features.table.BedTableCodec;
-import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
+import org.broadinstitute.sting.utils.codecs.table.BedTableCodec;
+import org.broadinstitute.sting.utils.codecs.table.TableFeature;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index bec0d5dd4..cec377f5f 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -7,7 +7,7 @@ import java.util.Arrays;
public class SelectVariantsIntegrationTest extends WalkerTest {
public static String baseTestString(String args) {
- return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s" + args;
+ return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s -NO_HEADER" + args;
}
@Test
@@ -16,7 +16,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
WalkerTestSpec spec = new WalkerTestSpec(
- baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant:VCF3 " + testfile + " -NO_HEADER"),
+ baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant:VCF3 " + testfile),
1,
Arrays.asList("d18516c1963802e92cb9e425c0b75fd6")
);
@@ -24,12 +24,26 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest("testComplexSelection--" + testfile, spec);
}
+ @Test
+ public void testSampleExclusion() {
+ String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
+ String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
+
+ WalkerTestSpec spec = new WalkerTestSpec(
+ "-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s -NO_HEADER -xl_sn A -xl_sf " + samplesFile + " --variant:VCF3 " + testfile,
+ 1,
+ Arrays.asList("730f021fd6ecf1d195dabbee2e233bfd")
+ );
+
+ executeTest("testSampleExclusion--" + testfile, spec);
+ }
+
@Test
public void testRepeatedLineSelection() {
String testfile = validationDataLocation + "test.dup.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
- baseTestString(" -sn A -sn B -sn C --variant:VCF3 " + testfile + " -NO_HEADER"),
+ baseTestString(" -sn A -sn B -sn C --variant:VCF3 " + testfile),
1,
Arrays.asList("b74038779fe6485dbb8734ae48178356")
);
diff --git a/settings/helpTemplates/style.css b/settings/helpTemplates/style.css
index 1d7bcc576..2abcf0397 100644
--- a/settings/helpTemplates/style.css
+++ b/settings/helpTemplates/style.css
@@ -95,6 +95,12 @@ dd {
padding: 0 0 0.5em 0;
}
+pre {
+ border: thin solid lightgray;
+ margin-left: 1em;
+ margin-right: 4em;
+ background-color: #e0fdff;
+}
/*
* clean table layouts
*/
@@ -128,6 +134,48 @@ dd {
}
th#row-divider
+{
+ font-weight: bolder;
+ font-size: larger;
+}
+
+
+/*
+ * Table design for input/ouptut description
+ */
+
+#description-table
+{
+ font-family: "Lucida Sans Unicode", "Lucida Grande", Sans-Serif;
+ font-size: 12px;
+ background: #fff;
+ margin: 5px;
+ border-collapse: collapse;
+ text-align: left;
+}
+#description-table th
+{
+ font-size: 16px;
+ font-weight: bold;
+ background-color: lightgray;
+ color: #039;
+ text-align: center;
+ padding: 10px 8px;
+ border-bottom: 2px solid #6678b1;
+}
+#description-table td
+{
+ border-bottom: 1px solid #ccc;
+ color: #669;
+ padding: 6px 8px;
+ text-align: right;
+}
+#description-table tbody tr:hover td
+{
+ color: #009;
+}
+
+th#row-divider
{
font-weight: bolder;
font-size: larger;