debug

bwapy/libbwapy.pyx

@@ -314,25 +314,26 @@ cdef class BwaAln:
         # this is `bwa aln`, and the rest is `bwa samse`
         bwa_cal_sa_reg_gap(0, self._index._bwt, num_seqs, seqs, opt._delegate)
 
-        # create the full alignment
-        for i in range(num_seqs):
-            s = &seqs[i]
-            # bwa_cal_sa_reg_gap frees name, seq, rseq, and qual, so add them back in again
-            self._copy_seq(queries[i], s)
-            bwa_aln2seq_core(s.n_aln, s.aln, s, 1, opt.max_hits)
-
-        # calculate the genomic position given the suffix array offsite
-        bwa_cal_pac_pos_with_bwt(self._index._bns, num_seqs, seqs, opt._delegate.max_diff, opt._delegate.fnr, self._index._bwt)
-
-        # TODO: can `_pacseq` be passed here?
-        # refine gapped alignment
-        bwa_refine_gapped(self._index._bns, num_seqs, seqs, NULL)
-
-        # create the AlignedSegment from FastxRecrod and bwa_seq_t.
-        recs = [
-            self._build_alignment(query=queries[i], seq=&seqs[i], kstr=kstr)
-            for i in range(num_seqs)
-        ]
+        # # create the full alignment
+        # for i in range(num_seqs):
+        #     s = &seqs[i]
+        #     # bwa_cal_sa_reg_gap frees name, seq, rseq, and qual, so add them back in again
+        #     self._copy_seq(queries[i], s)
+        #     bwa_aln2seq_core(s.n_aln, s.aln, s, 1, opt.max_hits)
+        #
+        # # calculate the genomic position given the suffix array offsite
+        # bwa_cal_pac_pos_with_bwt(self._index._bns, num_seqs, seqs, opt._delegate.max_diff, opt._delegate.fnr, self._index._bwt)
+        #
+        # # TODO: can `_pacseq` be passed here?
+        # # refine gapped alignment
+        # bwa_refine_gapped(self._index._bns, num_seqs, seqs, NULL)
+        #
+        # # create the AlignedSegment from FastxRecrod and bwa_seq_t.
+        # recs = [
+        #     self._build_alignment(query=queries[i], seq=&seqs[i], kstr=kstr)
+        #     for i in range(num_seqs)
+        # ]
+        recs = []
 
         bwa_free_read_seq(num_seqs, seqs)
         free(kstr)