From 3a5486325aa6037439591aa76136e703be217520 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 30 Jun 2017 15:39:05 -0400
Subject: [PATCH] r123: fixed a mem leak; more presets

---
 hit.c  |  1 +
 main.c | 14 ++++++++++++--
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/hit.c b/hit.c
index b6585d1..f367ef1 100644
--- a/hit.c
+++ b/hit.c
@@ -141,6 +141,7 @@ void mm_select_sub(void *km, float mask_level, float pri_ratio, int *n_, mm_reg1
 		for (i = k = 0; i < n; ++i)
 			if (r[i].parent == i || r[i].score >= r[r[i].parent].score * pri_ratio)
 				r[k++] = r[i];
+			else if (r[i].p) free(r[i].p);
 		if (k != n) mm_sync_regs(km, k, r); // removing hits requires sync()
 		*n_ = k;
 	}
diff --git a/main.c b/main.c
index dfe4ddc..8703e24 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r122-pre"
+#define MM_VERSION "2.0-r123-pre"
 
 void liftrlimit()
 {
@@ -109,13 +109,21 @@ int main(int argc, char *argv[])
 			else if (strcmp(optarg, "paf") == 0) opt.flag &= ~MM_F_OUT_SAM;
 			else {
 				fprintf(stderr, "[E::%s] unknown output format '%s'\n", __func__, optarg);
-				return 0;
+				return 1;
 			}
 		} else if (c == 'x') {
 			if (strcmp(optarg, "ava10k") == 0) {
 				opt.flag |= MM_F_AVA | MM_F_NO_SELF;
 				opt.min_chain_score = 100, opt.pri_ratio = 0.0f;
 				is_hpc = 1, k = 19, w = 5;
+			} else if (strcmp(optarg, "sam10k") == 0) {
+				opt.flag = MM_F_OUT_SAM | MM_F_CIGAR;
+				is_hpc = 1, k = 19;
+			} else if (strcmp(optarg, "paf10k") == 0) {
+				is_hpc = 1, k = 19;
+			} else {
+				fprintf(stderr, "[E::%s] unknown preset '%s'\n", __func__, optarg);
+				return 1;
 			}
 		}
 	}
@@ -141,6 +149,8 @@ int main(int argc, char *argv[])
 		fprintf(stderr, "    -p FLOAT   threshold to output a mapping [%g]\n", opt.pri_ratio);
 		fprintf(stderr, "    -x STR     preset (recommended to be applied before other options) []\n");
 		fprintf(stderr, "               ava10k: -Hk19 -Sw5 -p0 -m100 (PacBio/ONT all-vs-all read mapping)\n");
+		fprintf(stderr, "               sam10k: -Hk19 -Fsam (PacBio/ONT vs reference alignment)\n");
+		fprintf(stderr, "               paf10k: -Hk19 (PacBio/ONT vs reference mapping/alignment)\n");
 		fprintf(stderr, "  Alignment:\n");
 		fprintf(stderr, "    -A INT     matching score [%d]\n", opt.a);
 		fprintf(stderr, "    -B INT     mismatch penalty [%d]\n", opt.b);