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Merge remote-tracking branch 'remotes/khalid/rodRefactor' into rodRefactor 

Conflicts:
	public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
	public/java/test/org/broadinstitute/sting/BaseTest.java
This commit is contained in:
Mark DePristo 2011-08-07 10:32:27 -04:00
parent 573700d18d f049461120
commit 4d88e72958
5 changed files with 16 additions and 9 deletions
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12
build.xml
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@ -168,7 +168,7 @@
<target name="init.buildall">
<!-- Set the properties needed to build everything -->
<property name="gatk.target" value="private"/>
<!-- <property name="scala.target" value="core"/> -->
<property name="scala.target" value="core"/>
</target>
<target name="git.describe">
@ -977,11 +977,11 @@
<sourcepath path="${java.public.source.dir}"/>
<sourcepath path="${external.dir}"/>
</javadoc>
<!-- <javadoc destdir="javadoc" -->
<!-- classpathref="external.dependencies"> -->
<!-- <sourcepath path="${java.private.source.dir}"/> -->
<!-- <exclude name="**" unless="include.private" /> -->
<!-- </javadoc> -->
<javadoc destdir="javadoc"
classpathref="external.dependencies">
<sourcepath path="${java.private.source.dir}"/>
<exclude name="**" unless="include.private" />
</javadoc>
<mkdir dir="scaladoc"/>
<scaladoc srcdir="" destdir="scaladoc" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
<src path="${scala.public.source.dir}"/>

3
public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.walkers;
import org.broad.tribble.Feature;
import org.broad.tribble.dbsnp.DbSNPFeature;
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;
@ -71,7 +72,7 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
@Argument(fullName="showIndelPileups",shortName="show_indels",doc="In addition to base pileups, generate pileups of extended indel events")
public boolean SHOW_INDEL_PILEUPS = false;
@Argument(fullName="metadata",shortName="metadata",doc="Add these ROD bindings to the output Pileup", required=false)
@Input(fullName="metadata",shortName="metadata",doc="Add these ROD bindings to the output Pileup", required=false)
public List<RodBinding<Feature>> rods = Collections.emptyList();
public void initialize() {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -78,7 +78,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
@Argument(fullName="maskExtension", shortName="maskExtend", doc="How many bases beyond records from a provided 'mask' rod should variants be filtered; [default:0]", required=false)
protected Integer MASK_EXTEND = 0;
@Argument(fullName="maskName", shortName="mask", doc="The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call; [default:'Mask']", required=false)
@Argument(fullName="maskName", shortName="maskName", doc="The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call; [default:'Mask']", required=false)
protected String MASK_NAME = "Mask";
@Argument(fullName="missingValuesInExpressionsShouldEvaluateAsFailing", doc="When evaluating the JEXL expressions, should missing values be considered failing the expression (by default they are considered passing)?", required=false)

6
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -108,6 +108,12 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
@Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Don't include filtered loci.", required=false)
private boolean KEEP_ORIGINAL_CHR_COUNTS = false;
@Argument(fullName="discordance", shortName = "disc", doc="Output variants that were not called on a ROD comparison track", required=false)
private RodBinding<VariantContext> discordanceTrack = RodBinding.makeUnbound(VariantContext.class);
@Argument(fullName="concordance", shortName = "conc", doc="Output variants that were also called on a ROD comparison track", required=false)
private RodBinding<VariantContext> concordanceTrack = RodBinding.makeUnbound(VariantContext.class);
@Hidden
@Argument(fullName="keepAFSpectrum", shortName="keepAF", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false)
private boolean KEEP_AF_SPECTRUM = false;

2
public/java/test/org/broadinstitute/sting/BaseTest.java
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@ -64,7 +64,7 @@ public abstract class BaseTest {
public static final String b37Refseq = refseqAnnotationLocation + "refGene-big-table-b37.txt";
public static final String dbsnpDataLocation = GATKDataLocation;
public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_129_b36.vcf";
public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf";
public static final String b37dbSNP132 = dbsnpDataLocation + "dbsnp_132_b37.vcf";
public static final String hapmapDataLocation = comparisonDataLocation + "Validated/HapMap/3.3/";