Skip to content
Permalink
Browse files

Fix for oversplitting in assembleContigs (#519)

* Possible fix for oversplitting in assembleContigs .

* Changelog
  • Loading branch information...
dbolotin committed May 19, 2019
1 parent 846613b commit 83dd57e21969f62927fdc14fca1095b20f5577fa
@@ -1,2 +1,2 @@

Fix rare bug in export of imputed gene features
Fixes clone oversplitting in assembleContigs in noizy (e.g. single-cell) data with substanial fraction of sequences with errors in `CDR3`
Fixes rare bug in export of imputed gene feature sequences
@@ -64,6 +64,7 @@
import static io.repseq.core.GeneType.Variable;

/**
*
*/
public final class FullSeqAssembler {
private static int ABSENT_PACKED_VARIANT_INFO = -1;
@@ -1518,6 +1519,6 @@ else if (right == -1)
}

private boolean inSplitRegion(int p) {
return splitRegion == null || splitRegion.contains(p);
return splitRegion != null && splitRegion.contains(p);
}
}
@@ -8,7 +8,7 @@
"alignedSequenceEdgeDelta": 3,
"alignmentEdgeRegionSize": 7,
"minimalNonEdgePointsFraction": 0.25,
"subCloningRegion": "CDR3",
"subCloningRegion": null,
"trimmingParameters": {
"averageQualityThreshold": 20.0,
"windowSize": 8

0 comments on commit 83dd57e

Please sign in to comment.
You can’t perform that action at this time.