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Fix half-hearted attempt to try to move classes from package to package. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2389 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-12-17 17:41:42 +00:00
parent e6cc7dab26
commit 9143822822
5 changed files with 17 additions and 11 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java
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@ -1,8 +1,10 @@
package org.broadinstitute.sting.gatk.walkers; package org.broadinstitute.sting.gatk.walkers.qc;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
/** /**
* Walks over the input data set, calculating the total number of covered loci for diagnostic purposes. * Walks over the input data set, calculating the total number of covered loci for diagnostic purposes.

5
java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java
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@ -1,6 +1,9 @@
package org.broadinstitute.sting.gatk.walkers; package org.broadinstitute.sting.gatk.walkers.qc;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
/** /**
* Walks over the input data set, calculating the number of reads seen for diagnostic purposes. * Walks over the input data set, calculating the number of reads seen for diagnostic purposes.

8
java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java
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@ -1,9 +1,9 @@
package org.broadinstitute.sting.gatk.walkers; package org.broadinstitute.sting.gatk.walkers.qc;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.walkers.RefWalker;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
@ -26,8 +26,8 @@ public class CountRodByRefWalker extends RefWalker<CountRodWalker.Datum, Pair<Ex
public void initialize() { public void initialize() {
crw.verbose = verbose; crw.verbose = verbose;
crw.showSkipped = showSkipped; crw.showSkipped = showSkipped;
crw.out = out; JVMUtils.setFieldValue(JVMUtils.findField(CountRodWalker.class,"out"),crw,out);
crw.err = err; JVMUtils.setFieldValue(JVMUtils.findField(CountRodWalker.class,"err"),crw,err);
} }
public CountRodWalker.Datum map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public CountRodWalker.Datum map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {

3
java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java
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@ -1,10 +1,11 @@
package org.broadinstitute.sting.gatk.walkers; package org.broadinstitute.sting.gatk.walkers.qc;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.RODRecordList; import org.broadinstitute.sting.gatk.refdata.RODRecordList;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;

8
packages/GenomeAnalysisTK.xml
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@ -6,11 +6,11 @@
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class> <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<dependencies> <dependencies>
<package>org.broadinstitute.sting.gatk.filters</package> <package>org.broadinstitute.sting.gatk.filters</package>
<class>org.broadinstitute.sting.gatk.walkers.CountLociWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.CountReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker</class> <class>org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class> <class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class> <class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</class> <class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</class>
<!-- Quality scores recalibration --> <!-- Quality scores recalibration -->
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class> <class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
@ -66,11 +66,11 @@
</executable> </executable>
<resources> <resources>
<!-- GATK sample code and build scripts --> <!-- GATK sample code and build scripts -->
<file>java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java</file> <file>java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java</file> <file>java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java</file> <file>java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java</file> <file>java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file> <file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file> <file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>