making optimizations to funcotator

src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java

@@ -805,18 +805,24 @@ record = header.getProgramRecord(pgID);
     /**
      * A method to allow a user to inject data sources after initialization that were not specified as command-line
      * arguments.
+     *
+     * @param filePath path to the Feature file to register
+     * @param name what to call the Feature input
+     * @param featureType class of features
+     * @param featureQueryLookahead look ahead this many bases during queries that produce cache misses
      * @return The {@link FeatureInput} used as the key for this data source.
      */
     protected FeatureInput<? extends Feature> addFeatureInputsAfterInitialization(final String filePath,
                                                                                   final String name,
-                                                                                  final Class<? extends Feature> featureType) {
+                                                                                  final Class<? extends Feature> featureType,
+                                                                                  final int featureQueryLookahead) {
 
-        final FeatureInput<? extends Feature> featureInput = new FeatureInput<>(name + FeatureInput.FEATURE_ARGUMENT_TAG_DELIMITER + filePath);
+        final FeatureInput<? extends Feature> featureInput = new FeatureInput<>(filePath, name);
 
         //Add datasource to the feature manager too so that it can be queried. Setting lookahead to 0 to avoid caching.
         //Note: we are disabling lookahead here because of windowed queries that need to "look behind" as well.
         features.addToFeatureSources(
-                0,
+                featureQueryLookahead,
                 featureInput,
                 featureType,
                 cloudPrefetchBuffer,

src/main/java/org/broadinstitute/hellbender/tools/funcotator/Funcotator.java

@@ -211,7 +211,7 @@ public class Funcotator extends VariantWalker {
     /**
      * The current version of {@link Funcotator}.
      */
-    public static final String VERSION = "0.0.2";
+    public static final String VERSION = "0.0.3";
 
     //==================================================================================================================
     // Arguments:
@@ -568,9 +568,9 @@ private void initializeManualFeaturesForLocatableDataSources(final Map<Path, Pro
         }
     }
 
-    private void addFeaturesForLocatableDataSource( final Path dataSourceFile,
-                                                    final Properties dataSourceProperties,
-                                                    final Class<? extends Feature> featureClazz ) {
+    private void addFeaturesForLocatableDataSource(final Path dataSourceFile,
+                                                   final Properties dataSourceProperties,
+                                                   final Class<? extends Feature> featureClazz) {
 
         final String name = dataSourceProperties.getProperty(DataSourceUtils.CONFIG_FILE_FIELD_NAME_NAME);
 
@@ -580,7 +580,8 @@ private void addFeaturesForLocatableDataSource( final Path dataSourceFile,
                         IOUtils.getPath( dataSourceProperties.getProperty(DataSourceUtils.CONFIG_FILE_FIELD_NAME_SRC_FILE) )
                 ).toUri().toString(),
                 name,
-                featureClazz
+                featureClazz,
+                VariantWalkerBase.FEATURE_CACHE_LOOKAHEAD
         );
 
         // Add our feature input to our list of manual inputs:

src/main/java/org/broadinstitute/hellbender/utils/codecs/gencode/GencodeGtfCodec.java

@@ -139,16 +139,9 @@ public FeatureCodecHeader readHeader(final LineIterator lineIterator) throws IOE
         return new FeatureCodecHeader(readActualHeader(lineIterator), FeatureCodecHeader.NO_HEADER_END);
     }
 
-    @SuppressWarnings( "deprecation" )
     @Override
     public LocationAware makeIndexableSourceFromStream(final InputStream bufferedInputStream) {
-        final PositionalBufferedStream pbs;
-        if (bufferedInputStream instanceof PositionalBufferedStream) {
-            pbs = (PositionalBufferedStream) bufferedInputStream;
-        } else {
-            pbs = new PositionalBufferedStream(bufferedInputStream);
-        }
-        return new AsciiLineReaderIterator(new AsciiLineReader(pbs));
+        return new AsciiLineReaderIterator(AsciiLineReader.from(bufferedInputStream));
     }
 
     // ============================================================================================================

src/main/java/org/broadinstitute/hellbender/utils/codecs/gencode/GencodeGtfFeature.java

@@ -4,6 +4,7 @@
 import htsjdk.samtools.util.Locatable;
 import htsjdk.tribble.Feature;
 import htsjdk.tribble.annotation.Strand;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.broadinstitute.hellbender.exceptions.UserException;
@@ -108,23 +109,26 @@ protected GencodeGtfFeature(final String[] gtfFields) {
         // But we need to match up the field names to the fields themselves:
         for ( final String extraField : extraFields ) {
 
-            final String[] fieldParts = extraField.trim().split(EXTRA_FIELD_KEY_VALUE_SPLITTER);
+            final String trimmedExtraField = extraField.trim();
+            if (trimmedExtraField.isEmpty()) {
+                continue;
+            }
 
-            if ( fieldParts.length == 1 ){
-                if ( fieldParts[EXTRA_FIELD_KEY_INDEX].isEmpty() ){
-                    continue;
-                }
-                else {
-                    throw new UserException.MalformedFile("Extraneous optional field data - not in a key/value pair: " + extraField);
-                }
+            final int splitPoint = trimmedExtraField.indexOf(EXTRA_FIELD_KEY_VALUE_SPLITTER);
+            if( splitPoint == -1 ) {
+                throw new UserException.MalformedFile("Extraneous optional field data - not in a key/value pair: " + extraField);
             }
 
-            // Each optional field is in a key/value pair:
-            final String fieldName = fieldParts[EXTRA_FIELD_KEY_INDEX].trim();
+            final String fieldName = trimmedExtraField.substring(0, splitPoint).trim();
 
             // The value of the field may be between two quotes.
             // We remove them here.
-            final String fieldValue = fieldParts[EXTRA_FIELD_VALUE_INDEX].trim().replaceAll("\"", "");
+            final String rawFieldValue = trimmedExtraField.substring(splitPoint + 1, trimmedExtraField.length());
+            final String fieldValue = StringUtils.remove(rawFieldValue.trim(), '"');
+
+            if( fieldValue.contains(EXTRA_FIELD_KEY_VALUE_SPLITTER) ){
+                throw new UserException("Expected a key/value pair but found several values " + fieldName + "/" + fieldValue);
+            }
 
             OptionalField<?> optionalField = null;