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Added back the check for values.size() != header.size(). Now exception will be thrown if number of columns in a record doesn't equal number of columns in the header 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3473 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd 2010-06-02 16:23:05 +00:00
parent 290771a8c2
commit 12c3e3ecda
1 changed files with 7 additions and 7 deletions
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14
java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
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@ -32,6 +32,7 @@ import java.util.ArrayList;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broad.tribble.FeatureCodec; import org.broad.tribble.FeatureCodec;
import org.broad.tribble.exception.CodecLineParsingException;
import org.broad.tribble.util.AsciiLineReader; import org.broad.tribble.util.AsciiLineReader;
import org.broad.tribble.util.LineReader; import org.broad.tribble.util.LineReader;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
@ -64,7 +65,6 @@ public class AnnotatorInputTableCodec implements FeatureCodec<AnnotatorInputTabl
return lineCounter[0]; return lineCounter[0];
} }
@Override
public Class<AnnotatorInputTableFeature> getFeatureType() { public Class<AnnotatorInputTableFeature> getFeatureType() {
return AnnotatorInputTableFeature.class; return AnnotatorInputTableFeature.class;
} }
@ -79,9 +79,9 @@ public class AnnotatorInputTableCodec implements FeatureCodec<AnnotatorInputTabl
final ArrayList<String> header = this.header; //optimization final ArrayList<String> header = this.header; //optimization
final ArrayList<String> values = Utils.split(line, DELIMITER, header.size()); final ArrayList<String> values = Utils.split(line, DELIMITER, header.size());
//if ( values.size() > header.size()) { if ( values.size() != header.size()) {
// throw new CodecLineParsingException(String.format("Encountered a line within " + file + " that has %d columns which is > the number of columns in the header which has %d columns.\nHeader: " + header + "\nLine: " + values, values.size(), header.size())); throw new CodecLineParsingException(String.format("Encountered a line that has %d columns while the header has %d columns.\nHeader: " + header + "\nLine: " + values, values.size(), header.size()));
//} }
final AnnotatorInputTableFeature feature = new AnnotatorInputTableFeature(header); final AnnotatorInputTableFeature feature = new AnnotatorInputTableFeature(header);
for ( int i = 0; i < header.size(); i++ ) { for ( int i = 0; i < header.size(); i++ ) {
@ -132,8 +132,7 @@ public class AnnotatorInputTableCodec implements FeatureCodec<AnnotatorInputTabl
String line = null; String line = null;
while( (line = source.readLine()) != null ) { while( (line = source.readLine()) != null ) {
numLines++; numLines++;
line = line.trim(); if ( line.trim().isEmpty() || line.startsWith("#") ) {
if ( line.isEmpty() || line.startsWith("#") ) {
continue; continue;
} }
@ -150,7 +149,8 @@ public class AnnotatorInputTableCodec implements FeatureCodec<AnnotatorInputTabl
if(lineCounter != null) { if(lineCounter != null) {
lineCounter[0] = numLines; lineCounter[0] = numLines;
} }
logger.info(String.format("Found header line containing %d columns:\n[%s]", header.size(), Utils.join("\t", header)));
logger.debug(String.format("Found header line containing %d columns:\n[%s]", header.size(), Utils.join("\t", header)));
return header; return header;
} }