From 9bb785f066595076d4bf412bb7ff4566d616b4fb Mon Sep 17 00:00:00 2001
From: Nils Homer <nilshomer@gmail.com>
Date: Mon, 16 Dec 2024 10:43:49 -0700
Subject: [PATCH] debug

---
 bwapy/libbwapy.pyx | 43 +++++++++++++++++++++----------------------
 1 file changed, 21 insertions(+), 22 deletions(-)

diff --git a/bwapy/libbwapy.pyx b/bwapy/libbwapy.pyx
index 82aa64e..3f13018 100644
--- a/bwapy/libbwapy.pyx
+++ b/bwapy/libbwapy.pyx
@@ -265,27 +265,27 @@ cdef class BwaAln:
         if seq.type == BWA_TYPE_NO_MATCH:  # unmapped read
             # TODO: custom bwa tags: RG, BC, XC
             return rec
-        #
-        # ref_len_in_alignment = pos_end(seq) - seq.pos
-        #
-        # # if on the reverse strand, reverse the query sequence and qualities
-        # rec.query_sequence = query.sequence[::-1]
-        # if query.quality is not None:
-        #     rec.query_qualities = query.quality[::-1]
-        #
-        # # reference id
-        # nn = bns_cnt_ambi(self._index._bns, seq.pos, ref_len_in_alignment, &reference_id)
-        # rec.reference_id = reference_id
-        #
-        # # make this unmapped if we map off the end of the contig
-        # rec.is_unmapped = seq.pos + ref_len_in_alignment - self._index._bns.anns[
-        #     rec.reference_id].offset > self._index._bns.anns[rec.reference_id].len
-        #
-        # # strand, reference start, and mapping quality
-        # if seq.strand:
-        #     rec.is_reverse = True
-        # rec.reference_start = seq.pos - self._index._bns.anns[rec.reference_id].offset + 1
-        # rec.mapping_quality = seq.mapQ
+
+        ref_len_in_alignment = pos_end(seq) - seq.pos
+
+        # if on the reverse strand, reverse the query sequence and qualities
+        rec.query_sequence = query.sequence[::-1]
+        if query.quality is not None:
+            rec.query_qualities = query.quality[::-1]
+
+        # reference id
+        nn = bns_cnt_ambi(self._index._bns, seq.pos, ref_len_in_alignment, &reference_id)
+        rec.reference_id = reference_id
+
+        # make this unmapped if we map off the end of the contig
+        rec.is_unmapped = seq.pos + ref_len_in_alignment - self._index._bns.anns[
+            rec.reference_id].offset > self._index._bns.anns[rec.reference_id].len
+
+        # strand, reference start, and mapping quality
+        if seq.strand:
+            rec.is_reverse = True
+        rec.reference_start = seq.pos - self._index._bns.anns[rec.reference_id].offset + 1
+        rec.mapping_quality = seq.mapQ
         #
         # # cigar
         # cigar = ""
@@ -346,7 +346,6 @@ cdef class BwaAln:
             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)