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Found a small inefficiency while profiling: we were still using String.split instead of ParsingUtils.split to break up array values in the INFO field. There was a noticeable (albeit not big) difference in the change when reading sites only files.

This commit is contained in:
Eric Banks 2011-10-03 14:20:39 -04:00
parent c7898a9be7
commit c3eff7451a
2 changed files with 18 additions and 11 deletions
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28
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -36,6 +36,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
// for ParsingUtils.split
protected String[] GTValueArray = new String[100];
protected String[] genotypeKeyArray = new String[100];
protected String[] infoFieldArray = new String[1000];
protected String[] infoValueArray = new String[1000];
// for performance testing purposes
@ -351,23 +352,28 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
if ( infoField.indexOf("\t") != -1 || infoField.indexOf(" ") != -1 )
generateException("The VCF specification does not allow for whitespace in the INFO field");
int infoValueSplitSize = ParsingUtils.split(infoField, infoValueArray, VCFConstants.INFO_FIELD_SEPARATOR_CHAR);
for (int i = 0; i < infoValueSplitSize; i++) {
int infoFieldSplitSize = ParsingUtils.split(infoField, infoFieldArray, VCFConstants.INFO_FIELD_SEPARATOR_CHAR, false);
for (int i = 0; i < infoFieldSplitSize; i++) {
String key;
Object value;
int eqI = infoValueArray[i].indexOf("=");
int eqI = infoFieldArray[i].indexOf("=");
if ( eqI != -1 ) {
key = infoValueArray[i].substring(0, eqI);
String str = infoValueArray[i].substring(eqI+1, infoValueArray[i].length());
key = infoFieldArray[i].substring(0, eqI);
String str = infoFieldArray[i].substring(eqI+1);
// lets see if the string contains a , separator
if ( str.contains(",") )
value = Arrays.asList(str.split(","));
else
value = str;
// split on the INFO field separator
int infoValueSplitSize = ParsingUtils.split(str, infoValueArray, VCFConstants.INFO_FIELD_ARRAY_SEPARATOR_CHAR, false);
if ( infoValueSplitSize == 1 ) {
value = infoValueArray[0];
} else {
ArrayList<String> valueList = new ArrayList<String>(infoValueSplitSize);
for ( int j = 0; j < infoValueSplitSize; j++ )
valueList.add(infoValueArray[j]);
value = valueList;
}
} else {
key = infoValueArray[i];
key = infoFieldArray[i];
value = true;
}

1
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java
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@ -71,6 +71,7 @@ public final class VCFConstants {
public static final char FIELD_SEPARATOR_CHAR = '\t';
public static final String FILTER_CODE_SEPARATOR = ";";
public static final String INFO_FIELD_ARRAY_SEPARATOR = ",";
public static final char INFO_FIELD_ARRAY_SEPARATOR_CHAR = ',';
public static final String ID_FIELD_SEPARATOR = ";";
public static final String INFO_FIELD_SEPARATOR = ";";
public static final char INFO_FIELD_SEPARATOR_CHAR = ';';