From ab345e600b33897d563c5fea2e50ca1006e878fe Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Wed, 13 Dec 2017 12:23:43 -0500
Subject: [PATCH] r626: function to check incorrect scoring system

---
 main.c    |  4 +++-
 map.c     | 15 +++++++++++++++
 minimap.h |  1 +
 3 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/main.c b/main.c
index df996e7..da8ac7e 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.6-r625-dirty"
+#define MM_VERSION "2.6-r626-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -202,6 +202,8 @@ int main(int argc, char *argv[])
 	}
 	if (!fnw && !(opt.flag&MM_F_CIGAR))
 		ipt.flag |= MM_I_NO_SEQ;
+	if (mm_check_opt(&ipt, &opt) < 0)
+		return 1;
 
 	if (argc == optind || fp_help == stdout) {
 		fprintf(fp_help, "Usage: minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]\n");
diff --git a/map.c b/map.c
index 45e933c..b233211 100644
--- a/map.c
+++ b/map.c
@@ -115,6 +115,21 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 	return 0;
 }
 
+int mm_check_opt(const mm_idxopt_t *io, const mm_mapopt_t *mo)
+{
+	if (mo->a + 2 * (mo->q + mo->e) > 127 || mo->a + 2 * (mo->q2 + mo->e2) > 127) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m scoring system violating {-A}+2*({-O}+{-E}) <= 127\033[0m\n");
+		return -1;
+	}
+	if ((mo->q != mo->q2 || mo->e != mo->e2) && !(mo->e > mo->e2 && mo->q + mo->e < mo->q2 + mo->e2)) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m dual gap penalties violating E1>E2 and O1+E1<O2+E2\033[0m\n");
+		return -2;
+	}
+	return 0;
+}
+
 typedef struct {
 	uint32_t n;
 	uint32_t qpos;
diff --git a/minimap.h b/minimap.h
index b2783cb..32e1e1b 100644
--- a/minimap.h
+++ b/minimap.h
@@ -155,6 +155,7 @@ extern double mm_realtime0; // wall-clock timer
  * @return 0 if success; -1 if _present_ unknown
  */
 int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo);
+int mm_check_opt(const mm_idxopt_t *io, const mm_mapopt_t *mo);
 
 /**
  * Update mm_mapopt_t::mid_occ via mm_mapopt_t::mid_occ_frac