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Don't update lineNo for decodeLoc - only for decode (otherwise they get double-counted). Even still, because of the way the GATK currently utilizes Tribble we can parse the same line multiple times, which knocks the line counter out of sync. For now, I've added a TODO in the code to remind us and the error messages note that it's an approximate line number.

This commit is contained in:
Eric Banks 2011-12-14 10:43:52 -05:00
parent d3f4a5a901
commit 09a5a9eac0
2 changed files with 4 additions and 3 deletions
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3
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -184,7 +184,6 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
* @return a feature, (not guaranteed complete) that has the correct start and stop
*/
public Feature decodeLoc(String line) {
lineNo++;
// the same line reader is not used for parsing the header and parsing lines, if we see a #, we've seen a header line
if (line.startsWith(VCFHeader.HEADER_INDICATOR)) return null;
@ -279,6 +278,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
builder.source(getName());
// increment the line count
// TODO -- because of the way the engine utilizes Tribble, we can parse a line multiple times (especially when
// TODO -- the first record is far along the contig) and the line counter can get out of sync
lineNo++;
// parse out the required fields

4
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
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@ -184,11 +184,11 @@ public class UserException extends ReviewedStingException {
public static class MalformedVCF extends UserException {
public MalformedVCF(String message, String line) {
super(String.format("The provided VCF file is malformed at line %s: %s", line, message));
super(String.format("The provided VCF file is malformed at approximately line %s: %s", line, message));
}
public MalformedVCF(String message, int lineNo) {
super(String.format("The provided VCF file is malformed at line number %d: %s", lineNo, message));
super(String.format("The provided VCF file is malformed at approximately line number %d: %s", lineNo, message));
}
}