From 3c0d05d272b957289c5525790f718626131c2a96 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 6 Jan 2020 21:53:21 -0500
Subject: [PATCH] r962: abort given wrong RG line; resolves #541

---
 format.c | 12 ++++++++----
 main.c   | 12 +++++++++---
 mmpriv.h |  2 +-
 3 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/format.c b/format.c
index 6d9e7ab..0dd943a 100644
--- a/format.c
+++ b/format.c
@@ -79,11 +79,11 @@ static char *mm_escape(char *s)
 	return s;
 }
 
-static void sam_write_rg_line(kstring_t *str, const char *s)
+static int sam_write_rg_line(kstring_t *str, const char *s)
 {
 	char *p, *q, *r, *rg_line = 0;
 	memset(mm_rg_id, 0, 256);
-	if (s == 0) return;
+	if (s == 0) return 0;
 	if (strstr(s, "@RG") != s) {
 		if (mm_verbose >= 1) fprintf(stderr, "[ERROR] the read group line is not started with @RG\n");
 		goto err_set_rg;
@@ -108,20 +108,23 @@ static void sam_write_rg_line(kstring_t *str, const char *s)
 	for (q = p, r = mm_rg_id; *q && *q != '\t' && *q != '\n'; ++q)
 		*r++ = *q;
 	mm_sprintf_lite(str, "%s\n", rg_line);
+	return 0;
 
 err_set_rg:
 	free(rg_line);
+	return -1;
 }
 
-void mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int argc, char *argv[])
+int mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int argc, char *argv[])
 {
 	kstring_t str = {0,0,0};
+	int ret = 0;
 	if (idx) {
 		uint32_t i;
 		for (i = 0; i < idx->n_seq; ++i)
 			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);
+	if (rg) ret = sam_write_rg_line(&str, rg);
 	mm_sprintf_lite(&str, "@PG\tID:minimap2\tPN:minimap2");
 	if (ver) mm_sprintf_lite(&str, "\tVN:%s", ver);
 	if (argc > 1) {
@@ -132,6 +135,7 @@ void mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int
 	}
 	mm_err_puts(str.s);
 	free(str.s);
+	return ret;
 }
 
 static void write_cs_core(kstring_t *s, const uint8_t *tseq, const uint8_t *qseq, const mm_reg1_t *r, char *tmp, int no_iden, int write_tag)
diff --git a/main.c b/main.c
index 1b1fa81..2d8726e 100644
--- a/main.c
+++ b/main.c
@@ -7,7 +7,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.17-r961-dirty"
+#define MM_VERSION "2.17-r962-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -356,13 +356,19 @@ int main(int argc, char *argv[])
 			return 1;
 		}
 		if ((opt.flag & MM_F_OUT_SAM) && idx_rdr->n_parts == 1) {
+			int ret;
 			if (mm_idx_reader_eof(idx_rdr)) {
-				mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv);
+				ret = mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv);
 			} else {
-				mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
+				ret = mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
 				if (opt.split_prefix == 0 && mm_verbose >= 2)
 					fprintf(stderr, "[WARNING]\033[1;31m For a multi-part index, no @SQ lines will be outputted. Please use --split-prefix.\033[0m\n");
 			}
+			if (ret != 0) {
+				mm_idx_destroy(mi);
+				mm_idx_reader_close(idx_rdr);
+				return 1;
+			}
 		}
 		if (mm_verbose >= 3)
 			fprintf(stderr, "[M::%s::%.3f*%.2f] loaded/built the index for %d target sequence(s)\n",
diff --git a/mmpriv.h b/mmpriv.h
index c9b91cd..c1164e2 100644
--- a/mmpriv.h
+++ b/mmpriv.h
@@ -59,7 +59,7 @@ uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
 
 void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, int is_hpc, mm128_v *p);
 
-void mm_write_sam_hdr(const mm_idx_t *mi, const char *rg, const char *ver, int argc, char *argv[]);
+int mm_write_sam_hdr(const mm_idx_t *mi, const char *rg, const char *ver, int argc, char *argv[]);
 void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag);
 void mm_write_paf3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag, int rep_len);
 void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs);