ignore multi gene alignements (#74)

* ignore multi gene alignements

* (a) fixed the gene_name_tag to gene_id_tag in playform.py and (b) added the logic for multi genes when there is multiple genes

* fix linting

Co-authored-by: Kishori Konwar <kkonwar@broadinstitute.org>

src/sctools/count.py

@@ -290,13 +290,19 @@ def from_sorted_tagged_bam(
                 primary_alignment = alignments[0]
                 if primary_alignment.has_tag(gene_name_tag):
                     gene_name = primary_alignment.get_tag(gene_name_tag)
+                    # overlaps multiple genes, drop query, and unfortunately there only one
+                    # one alignment for this query
+                    if len(gene_name.split(',')) != 1:
+                        continue
                 else:
                     continue  # drop query
             else:  # multi-map
                 implicated_gene_names: Set[str] = set()
                 for alignment in alignments:
                     if alignment.has_tag(gene_name_tag):
-                        implicated_gene_names.add(alignment.get_tag(gene_name_tag))
+                        # consider its gene name only if it has only  gene name
+                        if len(gene_name.split(',')) == 1:
+                            implicated_gene_names.add(alignment.get_tag(gene_name_tag))
                 if len(implicated_gene_names) == 1:  # only one gene
                     gene_name = implicated_gene_names.__iter__().__next__()
                 else:

src/sctools/platform.py

@@ -450,7 +450,7 @@ def bam_to_count_matrix(cls, args: Iterable[str] = None) -> int:
             chromosomes_gene_locations_extended=gene_locations,
             cell_barcode_tag=args.cell_barcode_tag,
             molecule_barcode_tag=args.molecule_barcode_tag,
-            gene_name_tag=args.gene_name_tag,
+            gene_name_tag=args.gene_id_tag,
             open_mode=open_mode,
         )
         matrix.save(args.output_prefix)