update to use new samtools method
@@ -28,8 +28,7 @@ import org.opencb.biodata.models.core.*;
import org.opencb.biodata.models.variant.avro.Expression;
import org.opencb.biodata.models.variant.avro.GeneDrugInteraction;
import org.opencb.biodata.models.variant.avro.GeneTraitAssociation;
-import org.opencb.biodata.tools.sequence.FastaIndexManager;
-import org.opencb.biodata.tools.sequence.SamtoolsFastaIndex;
+import org.opencb.biodata.tools.sequence.FastaIndex;
import org.opencb.cellbase.core.config.SpeciesConfiguration;
import org.opencb.cellbase.core.exception.CellbaseException;
import org.opencb.cellbase.core.serializer.CellBaseSerializer;
@@ -174,7 +173,7 @@ public class GeneBuilder extends CellBaseBuilder {
// Preparing the fasta file for fast accessing
// FastaIndexManager fastaIndexManager = getFastaIndexManager();
- SamtoolsFastaIndex fastaIndex = new SamtoolsFastaIndex(genomeSequenceFilePath);
+ FastaIndex fastaIndex = new FastaIndex(genomeSequenceFilePath);
// Empty transcript and exon dictionaries
transcriptDict.clear();
@@ -459,15 +458,15 @@ public class GeneBuilder extends CellBaseBuilder {
}
}
- private FastaIndexManager getFastaIndexManager() throws Exception {
- FastaIndexManager fastaIndexManager;
- fastaIndexManager = new FastaIndexManager(genomeSequenceFilePath, true);
- if (!fastaIndexManager.isConnected()) {
- fastaIndexManager.index();
- }
-
- return fastaIndexManager;
- }
+// private FastaIndexManager getFastaIndexManager() throws Exception {
+// FastaIndexManager fastaIndexManager;
+// fastaIndexManager = new FastaIndexManager(genomeSequenceFilePath, true);
+// if (!fastaIndexManager.isConnected()) {
+// fastaIndexManager.index();
+// }
+//
+// return fastaIndexManager;
+// }
private void addGtfXrefs(Transcript transcript, Gene gene) {
List<Xref> xrefList = transcript.getXrefs();
