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Allow comments in a table-formatted file to precede the header line.

This commit is contained in:
Christopher Hartl 2011-11-09 15:27:38 -05:00
parent 11abb4f9d1
commit d828eba7f4
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
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@ -89,10 +89,10 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
boolean isFirst = true;
while ((line = reader.readLine()) != null) {
System.out.println(line);
if ( isFirst && ! line.startsWith(headerDelimiter) ) {
if ( isFirst && ! line.startsWith(headerDelimiter) && ! line.startsWith(commentDelimiter)) {
throw new UserException.MalformedFile("TableCodec file does not have a header");
}
isFirst &= false;
isFirst &= line.startsWith(commentDelimiter);
if (line.startsWith(headerDelimiter)) {
if (header.size() > 0) throw new IllegalStateException("Input table file seems to have two header lines. The second is = " + line);
String spl[] = line.split(delimiterRegex);