separated formating printing

for SAM in future; and for performance

mmpriv.h

@@ -2,6 +2,19 @@
 #define MMPRIV2_H
 
 #include "minimap.h"
+#include "bseq.h"
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+	unsigned l, m;
+	char *s;
+} kstring_t;
+#endif
 
 #ifdef __cplusplus
 extern "C" {
@@ -14,8 +27,8 @@ void radix_sort_128x(mm128_t *beg, mm128_t *end);
 void radix_sort_64(uint64_t *beg, uint64_t *end);
 uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
 
+void mm_write_paf(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, int which, mm_reg1_t *r);
 int mm_chain_dp(int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *a, uint64_t **_u, void *km);
-
 mm_reg1_t *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);
 
 #ifdef __cplusplus