From 1169600f6aaaa1ae0e7282098a20e7aacde88e66 Mon Sep 17 00:00:00 2001
From: Nils Homer <nilshomer@gmail.com>
Date: Mon, 16 Dec 2024 11:09:12 -0700
Subject: [PATCH] debug

---
 bwapy/libbwapy.pxd | 4 +++-
 bwapy/libbwapy.pyx | 6 +++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/bwapy/libbwapy.pxd b/bwapy/libbwapy.pxd
index e93d9a0..ee5e6dd 100644
--- a/bwapy/libbwapy.pxd
+++ b/bwapy/libbwapy.pxd
@@ -82,7 +82,7 @@ cdef extern from "bntseq.h":
 
 cdef extern from "kseq.h":
     ctypedef struct kstring_t:
-        pass
+        char *s
 
 cdef extern from "bwase.h":
     void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_main, int n_multi)
@@ -110,6 +110,8 @@ cdef extern from "bwtaln.h":
         int n_cigar
         int tid
         uint32_t full_len
+        uint32_t nm
+        char *md
 
 
     void bwa_free_read_seq(int n_seqs, bwa_seq_t *seqs)
diff --git a/bwapy/libbwapy.pyx b/bwapy/libbwapy.pyx
index 2a1289c..97c4862 100644
--- a/bwapy/libbwapy.pyx
+++ b/bwapy/libbwapy.pyx
@@ -301,9 +301,8 @@ cdef class BwaAln:
         # # tags
         if seq.type != BWA_TYPE_NO_MATCH:
             attrs = dict()
-            # attrs["MD"] = bwa_cal_md1(seq.n_cigar, seq.cigar, seq.len, seq.pos,
-            #                           seq.rseq if seq.strand else seq.seq, self._index._bns.l_pac,
-            #                           self._pacseq, kstr, &nm)
+            attrs["MD"] = f"{seq.md}"
+            attrs["NM"] = f"{seq.nm}"
             rec.set_tags(list(attrs.items()))
         # # TODO:the custom bwa tags: XT, NM, XN, SM, AM, X0, X1, XM, XO, XG, XA, HN
 
@@ -348,6 +347,7 @@ cdef class BwaAln:
         ]
 
         bwa_free_read_seq(num_seqs, seqs)
+        free(kstr.s)
         free(kstr)
 
         return recs