zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

We were never validating the sequence dictionary of tabix indexed VCFs for some reason. Fixed. 

These changes happened in Tribble, but Joel clobbered them with his commit.
We can now change the logging priority on failures to validate the sequence dictionary to WARN.
Thanks to Tim F for indirectly pointing this out.
This commit is contained in:
Eric Banks 2014-02-04 01:21:17 -05:00
parent 9cac24d1e6
commit 740b33acbb
2 changed files with 5 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java
View File

@ -96,7 +96,7 @@ public class IndexDictionaryUtils {
final ValidationExclusion.TYPE validationExclusionType ) {
// if the sequence dictionary is empty (as well as null which means it doesn't have a dictionary), skip validation
if (trackDict == null || trackDict.size() == 0)
logger.info("Track " + trackName + " doesn't have a sequence dictionary built in, skipping dictionary validation");
logger.warn("Track " + trackName + " doesn't have a sequence dictionary built in, skipping dictionary validation");
else {
Set<String> trackSequences = new TreeSet<String>();
for (SAMSequenceRecord dictionaryEntry : trackDict.getSequences())

5
public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java
View File

@ -34,6 +34,7 @@ import org.broad.tribble.TribbleException;
import org.broad.tribble.index.Index;
import org.broad.tribble.index.IndexFactory;
import org.broad.tribble.util.LittleEndianOutputStream;
import org.broad.tribble.util.TabixUtils;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
@ -171,7 +172,9 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
// we might not know the index type, try loading with the default reader constructor
logger.debug("Attempting to load " + inputFile + " as a tabix indexed file without validating it");
try {
return new Pair<AbstractFeatureReader, SAMSequenceDictionary>(AbstractFeatureReader.getFeatureReader(inputFile.getAbsolutePath(), createCodec(descriptor, name)),null);
final File indexFile = new File(inputFile.getAbsoluteFile() + TabixUtils.STANDARD_INDEX_EXTENSION);
final SAMSequenceDictionary dict = TabixUtils.getSequenceDictionary(indexFile);
return new Pair<>(AbstractFeatureReader.getFeatureReader(inputFile.getAbsolutePath(), createCodec(descriptor, name)), dict);
} catch (TribbleException e) {
throw new UserException(e.getMessage(), e);
}