separated formating printing

for SAM in future; and for performance

Makefile

@@ -3,7 +3,7 @@ CFLAGS=		-g -Wall -O2 -Wc++-compat -Wno-unused-function
 CPPFLAGS=
 INCLUDES=	-I.
 OBJS=		kalloc.o kthread.o misc.o bseq.o sketch.o chain.o align.o sdust.o \
-			index.o map.o ksw2_extz2_sse.o
+			index.o format.o map.o ksw2_extz2_sse.o
 PROG=		minimap2
 PROG_EXTRA=	sdust
 LIBS=		-lm -lz -lpthread
@@ -34,14 +34,15 @@ depend:
 
 # DO NOT DELETE
 
-align.o: minimap.h ksw2.h
+align.o: minimap.h mmpriv.h bseq.h ksw2.h
 bseq.o: bseq.h kseq.h
-chain.o: minimap.h mmpriv.h kalloc.h
+chain.o: minimap.h mmpriv.h bseq.h kalloc.h
+format.o: mmpriv.h minimap.h bseq.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
+map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h
 misc.o: minimap.h ksort.h
 sdust.o: kalloc.h kdq.h kvec.h sdust.h
 sketch.o: kvec.h kalloc.h minimap.h

align.c

@@ -4,10 +4,6 @@
 #include "mmpriv.h"
 #include "ksw2.h"
 
-#ifndef kroundup32
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
 static void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b)
 {
 	int i, j;

format.c

@@ -0,0 +1,72 @@
+#include <stdarg.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include "mmpriv.h"
+
+static inline void str_enlarge(kstring_t *s, int l)
+{
+	if (s->l + l + 1 > s->m) {
+		s->m = s->l + l + 1;
+		kroundup32(s->m);
+		s->s = (char*)realloc(s->s, s->m);
+	}
+}
+
+static inline void str_copy(kstring_t *s, const char *st, const char *en)
+{
+	str_enlarge(s, en - st);
+	memcpy(&s->s[s->l], st, en - st);
+	s->l += en - st;
+}
+
+static void mm_sprintf_lite(kstring_t *s, const char *fmt, ...)
+{
+	char buf[16]; // for integer to string conversion
+	const char *p, *q;
+	va_list ap;
+	va_start(ap, fmt);
+	for (q = p = fmt; *p; ++p) {
+		if (*p == '%') {
+			if (p > q) str_copy(s, q, p);
+			++p;
+			if (*p == 'd') {
+				int c, i, l = 0;
+				unsigned int x;
+				c = va_arg(ap, int);
+				x = c >= 0? c : -c;
+				do { buf[l++] = x%10 + '0'; x /= 10; } while (x > 0);
+				if (c < 0) buf[l++] = '-';
+				str_enlarge(s, l);
+				for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
+			} else if (*p == 's') {
+				char *r = va_arg(ap, char*);
+				str_copy(s, r, r + strlen(r));
+			} else if (*p == 'c') {
+				str_enlarge(s, 1);
+				s->s[s->l++] = va_arg(ap, int);
+			} else abort();
+			q = p + 1;
+		}
+	}
+	if (p > q) str_copy(s, q, p);
+	va_end(ap);
+	s->s[s->l] = 0;
+}
+
+void mm_write_paf(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, int which, mm_reg1_t *r)
+{
+	s->l = 0;
+	mm_sprintf_lite(s, "%s\t%d\t%d\t%d\t%c\t%s\t%d\t%d\t%d", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev], mi->seq[r->rid].name, mi->seq[r->rid].len, r->rs, r->re);
+	if (r->p) mm_sprintf_lite(s, "\t%d\t%d\t255", r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen);
+	else mm_sprintf_lite(s, "\t%d\t%d\t255", r->score, r->re - r->rs > r->qe - r->qs? r->re - r->rs : r->qe - r->qs);
+	mm_sprintf_lite(s, "\tcm:i:%d", r->cnt);
+	if (r->p) mm_sprintf_lite(s, "\ts1:i:%d", r->score);
+	if (r->parent == which) mm_sprintf_lite(s, "\ts2:i:%d", r->subsc);
+	if (r->p) {
+		uint32_t k;
+		mm_sprintf_lite(s, "\tNM:i:%d\tAS:i:%d\tnn:i:%d\tcg:Z:", r->p->n_diff, r->p->score, r->p->n_ambi);
+		for (k = 0; k < r->p->n_cigar; ++k)
+			mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MID"[r->p->cigar[k]&0xf]);
+	}
+}

map.c

@@ -4,7 +4,6 @@
 #include "kvec.h"
 #include "kalloc.h"
 #include "sdust.h"
-#include "minimap.h"
 #include "mmpriv.h"
 #include "bseq.h"
 
@@ -320,6 +319,7 @@ typedef struct {
 	const mm_mapopt_t *opt;
 	bseq_file_t *fp;
 	const mm_idx_t *mi;
+	kstring_t str;
 } pipeline_t;
 
 typedef struct {
@@ -368,22 +368,8 @@ static void *worker_pipeline(void *shared, int step, void *in)
 			bseq1_t *t = &s->seq[i];
 			for (j = 0; j < s->n_reg[i]; ++j) {
 				mm_reg1_t *r = &s->reg[i][j];
-				printf("%s\t%d\t%d\t%d\t%c\t", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev]);
-				if (mi->seq[r->rid].name) fputs(mi->seq[r->rid].name, stdout);
-				else printf("%d", r->rid + 1);
-				printf("\t%d\t%d\t%d", mi->seq[r->rid].len, r->rs, r->re);
-				if (r->p) printf("\t%d\t%d\t255", r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen);
-				else printf("\t%d\t%d\t255", r->score, r->re - r->rs > r->qe - r->qs? r->re - r->rs : r->qe - r->qs);
-				printf("\tcm:i:%d", r->cnt);
-				if (r->p) printf("\ts1:i:%d", r->score);
-				if (r->parent == j) printf("\ts2:i:%d", r->subsc);
-				if (r->p) {
-					uint32_t k;
-					printf("\tNM:i:%d\tAS:i:%d\tnn:i:%d\tcg:Z:", r->p->n_diff, r->p->score, r->p->n_ambi);
-					for (k = 0; k < r->p->n_cigar; ++k)
-						printf("%d%c", r->p->cigar[k]>>4, "MID"[r->p->cigar[k]&0xf]);
-				}
-				putchar('\n');
+				mm_write_paf(&p->str, mi, t, j, r);
+				puts(p->str.s);
 				free(r->p);
 			}
 			free(s->reg[i]);

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