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Renaming for consistency and bringing up to speed with new rod system

This commit is contained in:
Eric Banks 2011-08-17 13:28:19 -04:00
parent 6d629c176c
commit 575303ae6b
2 changed files with 45 additions and 12 deletions
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49
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRefWalker.java
View File

@ -25,7 +25,10 @@
package org.broadinstitute.sting.gatk.walkers.qc;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input;
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;
@ -33,25 +36,55 @@ import org.broadinstitute.sting.gatk.walkers.RefWalker;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.collections.Pair;
import java.util.Collections;
import java.util.List;
/**
* Prints out counts of the number of reference ordered data objects are
* each locus for debugging RefWalkers.
* Prints out counts of the number of reference ordered data objects encountered.
*
*
* <h2>Input</h2>
* <p>
* One or more rod files.
* </p>
*
* <h2>Output</h2>
* <p>
* Number of rods seen.
* </p>
*
* <h2>Examples</h2>
* <pre>
* java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
* -T CountRODsByRef \
* -o output.txt \
* --rod input.vcf
* </pre>
*
*/
public class CountRodByRefWalker extends RefWalker<CountRodWalker.Datum, Pair<ExpandingArrayList<Long>, Long>> {
@Argument(fullName = "verbose", shortName = "v", doc="If true, Countrod will print out detailed information about the rods it finds and locations", required = false)
public class CountRODsByRefWalker extends RefWalker<CountRODsWalker.Datum, Pair<ExpandingArrayList<Long>, Long>> {
/**
* One or more input rod files
*/
@Input(fullName="rod", shortName = "rod", doc="Input VCF file(s)", required=false)
public List<RodBinding<Feature>> rods = Collections.emptyList();
@Argument(fullName = "verbose", shortName = "v", doc="If true, this tool will print out detailed information about the rods it finds and locations", required = false)
public boolean verbose = false;
@Argument(fullName = "showSkipped", shortName = "s", doc="If true, CountRod will print out the skippped locations", required = false)
@Argument(fullName = "showSkipped", shortName = "s", doc="If true, this tool will print out the skipped locations", required = false)
public boolean showSkipped = false;
CountRodWalker crw = new CountRodWalker();
CountRODsWalker crw = new CountRODsWalker();
public void initialize() {
crw.verbose = verbose;
crw.showSkipped = showSkipped;
}
public CountRodWalker.Datum map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
public CountRODsWalker.Datum map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
return crw.map(tracker, ref, context);
}
@ -59,7 +92,7 @@ public class CountRodByRefWalker extends RefWalker<CountRodWalker.Datum, Pair<Ex
return crw.reduceInit();
}
public Pair<ExpandingArrayList<Long>, Long> reduce(CountRodWalker.Datum point, Pair<ExpandingArrayList<Long>, Long> sum) {
public Pair<ExpandingArrayList<Long>, Long> reduce(CountRODsWalker.Datum point, Pair<ExpandingArrayList<Long>, Long> sum) {
return crw.reduce(point, sum);
}
}

8
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsWalker.java
View File

@ -64,13 +64,13 @@ import java.util.*;
* <pre>
* java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
* -T CountRod \
* -T CountRODs \
* -o output.txt \
* --rod input.vcf
* </pre>
*
*/
public class CountRodWalker extends RodWalker<CountRodWalker.Datum, Pair<ExpandingArrayList<Long>, Long>> implements TreeReducible<Pair<ExpandingArrayList<Long>, Long>> {
public class CountRODsWalker extends RodWalker<CountRODsWalker.Datum, Pair<ExpandingArrayList<Long>, Long>> implements TreeReducible<Pair<ExpandingArrayList<Long>, Long>> {
@Output
public PrintStream out;
@ -80,10 +80,10 @@ public class CountRodWalker extends RodWalker<CountRodWalker.Datum, Pair<Expandi
@Input(fullName="rod", shortName = "rod", doc="Input VCF file(s)", required=false)
public List<RodBinding<Feature>> rods = Collections.emptyList();
@Argument(fullName = "verbose", shortName = "v", doc="If true, CountRod will print out detailed information about the rods it finds and locations", required = false)
@Argument(fullName = "verbose", shortName = "v", doc="If true, this tool will print out detailed information about the rods it finds and locations", required = false)
public boolean verbose = false;
@Argument(fullName = "showSkipped", shortName = "s", doc="If true, CountRod will print out the skipped locations", required = false)
@Argument(fullName = "showSkipped", shortName = "s", doc="If true, this tool will print out the skipped locations", required = false)
public boolean showSkipped = false;
@Override