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Resolving merge conflicts

This commit is contained in:
Eric Banks 2012-03-30 01:51:09 -04:00
parent 16bef191c6 962fc352ae
commit ad6ace2439
5 changed files with 12 additions and 9 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java
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@ -132,6 +132,7 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
private static final Collection<String> RIGHT_ALIGN_STRINGS = Arrays.asList(
"null",
"NA",
"unknown",
String.valueOf(Double.POSITIVE_INFINITY),
String.valueOf(Double.NEGATIVE_INFINITY),
String.valueOf(Double.NaN));
@ -144,7 +145,7 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
* @return true if the value is a right alignable
*/
protected static boolean isRightAlign(String value) {
return value == null || RIGHT_ALIGN_STRINGS.contains(value) || NumberUtils.isNumber(value);
return value == null || RIGHT_ALIGN_STRINGS.contains(value) || NumberUtils.isNumber(value.trim());
}
/**
@ -213,7 +214,7 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
public Object put(Object key, Object value) {
if (value != null) {
String formatted = formatValue(value);
if (!formatted.equals("")) {
if (!formatted.equals("") && !formatted.equals("unknown")) {
updateMaxWidth(formatted);
updateFormat(formatted);
}

4
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
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@ -60,6 +60,8 @@ public class GATKReportTable {
private static final String COULD_NOT_READ_DATA_LINE = "Could not read a data line of this table -- ";
private static final String COULD_NOT_READ_EMPTY_LINE = "Could not read the last empty line of this table -- ";
private static final String OLD_GATK_TABLE_VERSION = "We no longer support older versions of the GATK Tables";
private static final String NUMBER_CONVERSION_EXCEPTION = "String is a number but is not a long or a double: ";
public GATKReportTable(BufferedReader reader, GATKReportVersion version) {
int counter = 0;
@ -413,6 +415,8 @@ public class GATKReportTable {
// This code below is bs. Why am do I have to conform to bad code
// Below is some code to convert a string into its appropriate type.
// I second Roger's rant!
// If we got a string but the column is not a String type
Object newValue = null;

1
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk.traversals;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.WalkerManager;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
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@ -19,7 +19,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
*/
@Analysis(description = "The overlap between eval and comp sites")
public class CompOverlap extends VariantEvaluator implements StandardEval {
@DataPoint(description = "number of eval SNP sites", format = "%d")
@DataPoint(description = "number of eval variant sites", format = "%d")
long nEvalVariants = 0;
@DataPoint(description = "number of eval sites outside of comp sites", format = "%d")

9
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java
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@ -26,18 +26,17 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
import net.sf.picard.util.IntervalTree;
import org.apache.log4j.Logger;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.interval.IntervalUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
/**
* Stratifies the variants by whether they overlap an interval in the set provided on the command line.