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RodBinding source is no longer assumed to be a file

This commit is contained in:
Mark DePristo 2011-07-26 13:59:44 -04:00
parent d0badd5bd6
commit 9dfb57168a
2 changed files with 7 additions and 7 deletions
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12
public/java/src/org/broadinstitute/sting/commandline/RodBinding.java
View File

@ -33,19 +33,19 @@ import java.util.List;
*/ */
public class RodBinding { public class RodBinding {
final String variableName; final String variableName;
final String sourceFile; final String source;
public RodBinding(final String variableName, final String sourceFile) { public RodBinding(final String variableName, final String source) {
this.variableName = variableName; this.variableName = variableName;
this.sourceFile = sourceFile; this.source = source;
} }
public String getVariableName() { public String getVariableName() {
return variableName; return variableName;
} }
public String getSourceFile() { public String getSource() {
return sourceFile; return source;
} }
public List<Object> getAll(RefMetaDataTracker tracker) { public List<Object> getAll(RefMetaDataTracker tracker) {
@ -53,7 +53,7 @@ public class RodBinding {
} }
public String toString() { public String toString() {
return String.format("(RodBinding name=%s source=%s)", variableName, sourceFile); return String.format("(RodBinding name=%s source=%s)", getVariableName(), getSource());
} }
} }

2
public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java
View File

@ -146,7 +146,7 @@ public class ListFileUtils {
Collection<RMDTriplet> rodBindings = new ArrayList<RMDTriplet>(); Collection<RMDTriplet> rodBindings = new ArrayList<RMDTriplet>();
for (RodBinding rodBinding: RODBindings) { for (RodBinding rodBinding: RODBindings) {
String argValue = rodBinding.getSourceFile().getPath(); String argValue = rodBinding.getSource();
String fileName = expandFileName(argValue); String fileName = expandFileName(argValue);
final Tags tags = parser.getTags(rodBinding); final Tags tags = parser.getTags(rodBinding);