Remove primary alignments stat

Author: BioWilko

bin/generate_alignment_report.py

@@ -47,7 +47,6 @@ def generate_bam_stats(bam_file: str) -> dict:
                 "num_reads": 0,
                 "forward_reads": 0,
                 "unique_mappers": 0,
-                "primary_alignments": 0,
             },
         )
         stats_dict[ref_name]["num_reads"] += 1
@@ -70,9 +69,6 @@ def generate_bam_stats(bam_file: str) -> dict:
             stats_dict[ref_name]["start_end_positions"].setdefault(start_end_tuple, 0)
             stats_dict[ref_name]["start_end_positions"][start_end_tuple] += 1
 
-            if not read.is_secondary:
-                stats_dict[ref_name]["primary_alignments"] += 1
-
             stats_dict[ref_name]["identities"].append(identity)
             stats_dict[ref_name]["alignment_lengths"].append(aln_length)
             stats_dict[ref_name]["read_lengths"].append(read.infer_read_length())
@@ -119,7 +115,6 @@ def generate_bam_stats(bam_file: str) -> dict:
             "mean_aln_length": mean_aln_length if mean_aln_length > 0 else 0,
             "forward_proportion": forward_proportion if forward_proportion > 0 else 0,
             "uniquely_mapped_reads": stats["unique_mappers"],
-            "primary_alignments": stats["primary_alignments"],
             "mean_read_length": round(np.mean(stats["read_lengths"]), 2),
             "mean_alignment_proportion": round(
                 np.mean(stats["alignment_proportions"]), 2
@@ -303,7 +298,6 @@ def run(args):
             "coverage_10x",
             "mapped_reads",
             "uniquely_mapped_reads",
-            "primary_alignments",
             "mapped_bases",
             "mean_read_identity",
             "read_duplication_rate",
@@ -335,7 +329,6 @@ def run(args):
             stats["mean_alignment_length"] = bam_stats[ref]["mean_aln_length"]
             stats["forward_proportion"] = bam_stats[ref]["forward_proportion"]
             stats["uniquely_mapped_reads"] = bam_stats[ref]["uniquely_mapped_reads"]
-            stats["primary_alignments"] = bam_stats[ref]["primary_alignments"]
             stats["mean_read_length"] = bam_stats[ref]["mean_read_length"]
             stats["mean_alignment_proportion"] = bam_stats[ref][
                 "mean_alignment_proportion"