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some tweaks for the GATK paper genotyper to better work with shared memory parallelization, added documentation changes for Matt's new help system. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2319 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-12-10 22:33:51 +00:00
parent a7cd172628
commit f64a4c66ac
3 changed files with 13 additions and 10 deletions
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2
java/src/org/broadinstitute/sting/gatk/traversals/TraverseLocusWindows.java
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@ -17,7 +17,7 @@ import java.util.List;
/** /**
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.
* User: amckenna * User: ebanks
* Date: Apr 23, 2009 * Date: Apr 23, 2009
* Time: 10:26:03 AM * Time: 10:26:03 AM
* To change this template use File | Settings | File Templates. * To change this template use File | Settings | File Templates.

17
java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java
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@ -6,20 +6,19 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotypePriors; import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotypePriors;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.io.PrintWriter; import java.io.PrintStream;
/** /**
* @author aaron * @author aaron
* <p/> * A simple Bayesian genotyper, that output a text based call format. Intended to be used only as an
* Class GATKPaperGenotyper * example in the GATK publication.
* <p/> *
* A simple Bayesian genotyper, that output a text based call format. Intended to be used only as an * @help.description A simple, naive Bayesian genotyper that is used as an example locus walker in the GATK paper. THIS IS NOT TO BE USED FOR ANY ANALYSIS
* example in the GATK publication.
*/ */
public class GATKPaperGenotyper extends LocusWalker<SimpleCall, Integer> implements TreeReducible<Integer> { public class GATKPaperGenotyper extends LocusWalker<SimpleCall, Integer> implements TreeReducible<Integer> {
@ -28,7 +27,7 @@ public class GATKPaperGenotyper extends LocusWalker<SimpleCall, Integer> impleme
// where to write the genotyping data to // where to write the genotyping data to
@Argument(fullName = "call_location", shortName = "cl", doc = "File to which calls should be written", required = true) @Argument(fullName = "call_location", shortName = "cl", doc = "File to which calls should be written", required = true)
public PrintWriter outputStream; public PrintStream outputStream;
/** /**
* our map function, which takes the reads spanning this locus, any associated reference ordered data, * our map function, which takes the reads spanning this locus, any associated reference ordered data,
@ -90,7 +89,7 @@ public class GATKPaperGenotyper extends LocusWalker<SimpleCall, Integer> impleme
* @return accumulator with result of the map taken into account. * @return accumulator with result of the map taken into account.
*/ */
public Integer reduce(SimpleCall value, Integer sum) { public Integer reduce(SimpleCall value, Integer sum) {
outputStream.println(value.toString()); if (value != null) outputStream.println(value.toString());
return sum + 1; return sum + 1;
} }

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/package-info.java 100644
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@ -0,0 +1,4 @@
/**
* @help.display.name The GATK paper's Bayesian genotyper
*/
package org.broadinstitute.sting.playground.gatk.walkers.papergenotyper;