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fulcrumgenomics · Jan 18, 2025 · 97d5aaa · 97d5aaa
1 parent 2c0d544
commit 97d5aaa
Showing 1 changed file with 19 additions and 1 deletion.
diff --git a/pybwa/libbwamem.pyx b/pybwa/libbwamem.pyx
@@ -826,19 +826,29 @@ cdef class BwaMem:
             query = queries[i]
             mem_alns = &mem_alns_vec[i]
 
+            sys.stderr.write(f"[loop] start i={i}\n")
+            sys.stderr.flush()
+
             mapped_recs = []
             for j in range(mem_alns.n):
+                sys.stderr.write(f"[loop] start i={i} j={j}\n")
+                sys.stderr.flush()
                 rec = self._unmapped(query=query)
 
+
                 mem_aln = mem_alns.a[j]
 
                 # set the flags
                 mem_aln.flag |= 0x4 if mem_aln.rid < 0 else 0
                 mem_aln.flag |= 0x10 if mem_aln.is_rev > 0 else 0
                 rec.flag = (mem_aln.flag & 0xffff) | (0x100 if (mem_aln.flag & 0x10000) != 0 else 0)
                 if rec.is_unmapped:
+                    sys.stderr.write(f"[loop] unmapped i={i} j={j}\n")
+                    sys.stderr.flush()
                     continue
 
+                sys.stderr.write(f"[loop] mapped i={i} j={j}\n")
+                sys.stderr.flush()
                 # for secondary alignments, do not add sequence and qualities
                 if rec.is_secondary:
                     rec.query_sequence = None
@@ -904,24 +914,32 @@ cdef class BwaMem:
 
                 mapped_recs.append(rec)
 
+            sys.stderr.write(f"[loop] free'ing mem_aln and XA i={i}\n")
+            sys.stderr.flush()
             for j in range(mem_alns.n):
                 mem_aln = mem_alns.a[j]
                 free(mem_aln.cigar)
                 free(mem_aln.XA)
+            sys.stderr.write(f"[loop] end free'ing mem_aln and XA i={i}\n")
             if len(mapped_recs) == 0:
                 recs_to_return.append([self._unmapped(query=query)])
             else:
                 self._add_sa_tag(mapped_recs)
                 recs_to_return.append(mapped_recs)
+            sys.stderr.write(f"[loop] end free'ing mem_alnregs.a i={i}\n")
             free(mem_alnregs.a)
 
+        sys.stderr.write(f"[loop] end free'ing\n")
         for i in range(num_seqs):
+            sys.stderr.write(f"[loop] end free'ing seqs {i}\n")
             free(seqs[i].name)
             free(seqs[i].comment)
             free(seqs[i].seq)
             free(seqs[i].qual)
+            sys.stderr.write(f"[loop] end free'ing mem_alns_vec[i].a {i}\n")
             free(mem_alns_vec[i].a)
-        free(mem_alns_vec)
         free(seqs)
+        sys.stderr.write(f"[loop] end free'ing mem_alns_vec {i}\n")
+        free(mem_alns_vec)
 
         return recs_to_return