From 326d91deb01827ea51ddc1066aa0af244dace292 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 23 Jun 2017 14:06:00 -0400
Subject: [PATCH] backup

---
 Makefile  | 2 ++
 align.c   | 5 ++++-
 minimap.h | 4 ++--
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/Makefile b/Makefile
index 44ce80c..184ab6b 100644
--- a/Makefile
+++ b/Makefile
@@ -33,10 +33,12 @@ depend:
 
 # DO NOT DELETE
 
+align.o: minimap.h ksw2.h
 bseq.o: bseq.h kseq.h
 chain.o: minimap.h mmpriv.h kalloc.h
 index.o: kthread.h bseq.h minimap.h mmpriv.h kvec.h kalloc.h khash.h
 kalloc.o: kalloc.h
+ksw2_extz2_sse.o: ksw2.h
 main.o: bseq.h minimap.h mmpriv.h
 map.o: kthread.h kvec.h kalloc.h sdust.h minimap.h mmpriv.h bseq.h
 misc.o: minimap.h ksort.h
diff --git a/align.c b/align.c
index d3c04d4..e56fc99 100644
--- a/align.c
+++ b/align.c
@@ -5,7 +5,7 @@
 void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int n_regs, mm_reg1_t *regs, mm128_t *a)
 {
 	extern unsigned char seq_nt4_table[256];
-	int i, reg;
+	int i, k, reg;
 	uint8_t *qseq0[2];
 
 	qseq0[0] = (uint8_t*)kmalloc(km, qlen);
@@ -30,6 +30,9 @@ void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 			qseq = &qseq0[rev][qs];
 			ret = mm_idx_getseq(mi, rid, rs, re, tseq);
 			assert(ret > 0);
+			fprintf(stderr, "===> %d,%d (%s:%d-%d) <===\n", reg, i, mi->seq[rid].name, rs, re);
+			for (k = 0; k < re - rs; ++k) fputc("ACGTN"[tseq[k]], stderr); fputc('\n', stderr);
+			for (k = 0; k < qe - qs; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
 		}
 		kfree(km, tseq);
 	}
diff --git a/minimap.h b/minimap.h
index d886f8c..5ab9c6a 100644
--- a/minimap.h
+++ b/minimap.h
@@ -74,8 +74,8 @@ typedef struct mm_tbuf_s mm_tbuf_t;
 
 struct bseq_file_s;
 
-#define mm_seq4_set(s, i, c) ((s)[(i)>>8] |= (uint32_t)(c) << (((i)&7)<<2))
-#define mm_seq4_get(s, i)    ((s)[(i)>>8] >> (((i)&7)<<2) & 0xf)
+#define mm_seq4_set(s, i, c) ((s)[(i)>>4] |= (uint32_t)(c) << (((i)&7)<<2))
+#define mm_seq4_get(s, i)    ((s)[(i)>>4] >> (((i)&7)<<2) & 0xf)
 
 #ifdef __cplusplus
 extern "C" {