From 623b5d9d48ecc9ed6755c85de2f02a778d5cb501 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 22 Mar 2018 11:31:58 -0400
Subject: [PATCH] r750: check puts() return (#132 & #103)

---
 format.c |  5 ++---
 main.c   |  7 ++++++-
 map.c    |  6 +++---
 misc.c   | 11 +++++++++++
 mmpriv.h |  2 ++
 5 files changed, 24 insertions(+), 7 deletions(-)

diff --git a/format.c b/format.c
index 89a93b6..712e560 100644
--- a/format.c
+++ b/format.c
@@ -118,7 +118,7 @@ void mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int
 	if (idx) {
 		uint32_t i;
 		for (i = 0; i < idx->n_seq; ++i)
-			printf("@SQ\tSN:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len);
+			mm_sprintf_lite(&str, "@SQ\tSN:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len);
 	}
 	if (rg) sam_write_rg_line(&str, rg);
 	mm_sprintf_lite(&str, "@PG\tID:minimap2\tPN:minimap2");
@@ -129,8 +129,7 @@ void mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int
 		for (i = 1; i < argc; ++i)
 			mm_sprintf_lite(&str, " %s", argv[i]);
 	}
-	mm_sprintf_lite(&str, "\n");
-	fputs(str.s, stdout);
+	mm_err_puts(str.s);
 	free(str.s);
 }
 
diff --git a/main.c b/main.c
index 9b07eb8..b6f75e8 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "getopt.h"
 #endif
 
-#define MM_VERSION "2.9-r749-dirty"
+#define MM_VERSION "2.9-r750-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -336,6 +336,11 @@ int main(int argc, char *argv[])
 	}
 	mm_idx_reader_close(idx_rdr);
 
+	if (fflush(stdout) == EOF) {
+		fprintf(stderr, "[ERROR] failed to write the results\n");
+		exit(EXIT_FAILURE);
+	}
+
 	if (mm_verbose >= 3) {
 		fprintf(stderr, "[M::%s] Version: %s\n", __func__, MM_VERSION);
 		fprintf(stderr, "[M::%s] CMD:", __func__);
diff --git a/map.c b/map.c
index 4dcff71..3146678 100644
--- a/map.c
+++ b/map.c
@@ -489,11 +489,11 @@ static void *worker_pipeline(void *shared, int step, void *in)
 						mm_write_sam2(&p->str, mi, t, i - seg_st, j, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag);
 					else
 						mm_write_paf(&p->str, mi, t, r, km, p->opt->flag);
-					puts(p->str.s);
+					mm_err_puts(p->str.s);
 				}
-				if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) {
+				if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) { // write an unmapped record
 					mm_write_sam2(&p->str, mi, t, i - seg_st, -1, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag);
-					puts(p->str.s);
+					mm_err_puts(p->str.s);
 				}
 			}
 			for (i = seg_st; i < seg_en; ++i) {
diff --git a/misc.c b/misc.c
index acf2f6c..f7a43cb 100644
--- a/misc.c
+++ b/misc.c
@@ -1,3 +1,4 @@
+#include <stdlib.h>
 #include "mmpriv.h"
 
 int mm_verbose = 1;
@@ -120,6 +121,16 @@ double realtime(void)
 	return tp.tv_sec + tp.tv_usec * 1e-6;
 }
 
+void mm_err_puts(const char *str)
+{
+	int ret;
+	ret = puts(str);
+	if (ret == EOF) {
+		fprintf(stderr, "[ERROR] failed to write the results\n");
+		exit(EXIT_FAILURE);
+	}
+}
+
 #include "ksort.h"
 
 #define sort_key_128x(a) ((a).x)
diff --git a/mmpriv.h b/mmpriv.h
index 4a1ae2b..c3c9a6d 100644
--- a/mmpriv.h
+++ b/mmpriv.h
@@ -86,6 +86,8 @@ mm_seg_t *mm_seg_gen(void *km, uint32_t hash, int n_segs, const int *qlens, int
 void mm_seg_free(void *km, int n_segs, mm_seg_t *segs);
 void mm_pair(void *km, int max_gap_ref, int dp_bonus, int sub_diff, int match_sc, const int *qlens, int *n_regs, mm_reg1_t **regs);
 
+void mm_err_puts(const char *str);
+
 #ifdef __cplusplus
 }
 #endif