Merge pull request #175 from naobservatory/will-fix-unpaired

Removed UP check from process_viral_bowtie2_sam.py

modules/local/processViralBowtie2Sam/resources/usr/bin/process_viral_bowtie2_sam.py

@@ -341,13 +341,10 @@ def process_paired_sam(inf, outf, genbank_metadata, viral_taxids):
             fwd_line = rev_line
             rev_line = get_next_alignment(inf)
             continue
-        # Check that pair statuses match and are valid
+        # Check that pair statuses match
         if rev_dict["pair_status"] != fwd_dict["pair_status"]:
             msg = f"Pair status mismatch: {fwd_dict['query_name']}, {fwd_dict['pair_status']}, {rev_dict['pair_status']}"
             raise ValueError(msg)
-        if fwd_dict["pair_status"] == "UP" or rev_dict["pair_status"] == "UP":
-            msg = f"Both mates align but alignment is unpaired: {fwd_dict['query_name']}"
-            raise ValueError(msg)
         # Process pair together
         line = line_from_pair(fwd_dict, rev_dict)
         outf.write(line)