57 lines
2.3 KiB
Java
Executable File
57 lines
2.3 KiB
Java
Executable File
package org.broadinstitute.sting.oneoffprojects.walkers;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.refdata.*;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.*;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import java.util.EnumSet;
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/**
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* Test routine for new VariantContext object
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*/
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public class TestVariantContextWalker extends RodWalker<Integer, Integer> {
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@Argument(fullName="takeFirstOnly", doc="Only take the first second at a locus, as opposed to all", required=false)
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boolean takeFirstOnly = false;
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@Argument(fullName="onlyContextsOfType", doc="Only take variant contexts of this type", required=false)
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VariantContext.Type onlyOfThisType = null;
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@Argument(fullName="onlyContextsStartinAtCurrentPosition", doc="Only take variant contexts at actually start at the current position, excluding those at span to the current location but start earlier", required=false)
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boolean onlyContextsStartinAtCurrentPosition = false;
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@Argument(fullName="printPerLocus", doc="If true, we'll print the variant contexts, in addition to counts", required=false)
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boolean printContexts = false;
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( ref == null )
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return 0;
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else {
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EnumSet<VariantContext.Type> allowedTypes = onlyOfThisType == null ? null : EnumSet.of(onlyOfThisType);
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int n = 0;
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for (VariantContext vc : tracker.getAllVariantContexts(allowedTypes, context.getLocation(), onlyContextsStartinAtCurrentPosition, takeFirstOnly) ) {
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n++;
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if ( printContexts ) out.printf(" %s%n", vc);
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}
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if ( n > 0 && printContexts ) {
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out.printf("%s => had %d variant context objects%n", context.getLocation(), n);
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out.printf("---------------------------------------------%n");
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}
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return n;
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}
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}
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public Integer reduceInit() {
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return 0;
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}
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public Integer reduce(Integer point, Integer sum) {
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return point + sum;
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}
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} |