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Adding options to warn instead of erroring out (so that you can see all errors in one shot) and to skip filtered records 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5042 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-01-21 05:24:28 +00:00
parent 02b5d4357f
commit 78a43faebe
1 changed files with 21 additions and 2 deletions
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23
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
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@ -60,6 +60,14 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
@Argument(fullName = "validationType", shortName = "type", doc = "which validation type to run", required = false) @Argument(fullName = "validationType", shortName = "type", doc = "which validation type to run", required = false)
protected ValidationType type = ValidationType.ALL; protected ValidationType type = ValidationType.ALL;
@Argument(fullName = "doNotValidateFilteredRecords", shortName = "doNotValidateFilteredRecords", doc = "should we skip validation on filtered records?", required = false)
protected Boolean DO_NOT_VALIDATE_FILTERED = false;
@Argument(fullName = "warnOnErrors", shortName = "warnOnErrors", doc = "should we just emit warnings on errors instead of terminating the run?", required = false)
protected Boolean WARN_ON_ERROR = false;
private long numErrors = 0;
private File file = null; private File file = null;
public void initialize() { public void initialize() {
@ -87,10 +95,16 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
public Integer reduce(Integer value, Integer sum) { return sum+value; } public Integer reduce(Integer value, Integer sum) { return sum+value; }
public void onTraversalDone(Integer result) { public void onTraversalDone(Integer result) {
System.out.println("Successfully validated the input file. Checked " + result + " records with no failures."); if ( numErrors == 0 )
System.out.println("Successfully validated the input file. Checked " + result + " records with no failures.");
else
System.out.println("Found " + numErrors + " records with failures.");
} }
private void validate(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref) { private void validate(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref) {
if ( DO_NOT_VALIDATE_FILTERED && vc.isFiltered() )
return;
// get the true reference allele // get the true reference allele
Allele reportedRefAllele = vc.getReference(); Allele reportedRefAllele = vc.getReference();
Allele observedRefAllele; Allele observedRefAllele;
@ -149,7 +163,12 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
break; break;
} }
} catch (TribbleException e) { } catch (TribbleException e) {
throw new UserException.MalformedFile(file, e.getMessage()); if ( WARN_ON_ERROR ) {
numErrors++;
logger.warn("***** " + e.getMessage() + " *****");
} else {
throw new UserException.MalformedFile(file, e.getMessage());
}
} }
} }
} }