From 640b1a17278b0d024f03ecb5521c9ff0f15c586f Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 26 Jun 2017 11:41:09 -0400
Subject: [PATCH] command-line option to control CIGAR output

---
 main.c    | 9 ++++++---
 map.c     | 3 ++-
 minimap.h | 3 ++-
 3 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/main.c b/main.c
index 6764255..ca60d6a 100644
--- a/main.c
+++ b/main.c
@@ -9,7 +9,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r36-pre"
+#define MM_VERSION "2.0-r74-pre"
 
 void liftrlimit()
 {
@@ -54,7 +54,7 @@ int main(int argc, char *argv[])
 	mm_realtime0 = realtime();
 	mm_mapopt_init(&opt);
 
-	while ((c = getopt(argc, argv, "w:k:B:b:t:r:f:Vv:Ng:I:d:ST:s:Dx:Hp:m:z:F:")) >= 0) {
+	while ((c = getopt(argc, argv, "w:k:B:b:t:r:f:Vv:Ng:I:d:ST:s:Dx:Hcp:m:z:F:")) >= 0) {
 		if (c == 'w') w = atoi(optarg);
 		else if (c == 'k') k = atoi(optarg);
 		else if (c == 'b') b = atoi(optarg);
@@ -68,6 +68,7 @@ int main(int argc, char *argv[])
 		else if (c == 'N') keep_name = 0;
 		else if (c == 'p') opt.pri_ratio = atof(optarg);
 		else if (c == 'm') opt.mask_level = atof(optarg);
+		else if (c == 'c') opt.flag |= MM_F_CIGAR;
 		else if (c == 'D') opt.flag |= MM_F_NO_SELF;
 		else if (c == 'S') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
 		else if (c == 'T') opt.sdust_thres = atoi(optarg);
@@ -86,7 +87,7 @@ int main(int argc, char *argv[])
 			if (c == 'B') mini_batch_size = (uint64_t)(x + .499);
 			else batch_size = (uint64_t)(x + .499);
 		} else if (c == 'F') {
-			if (strcmp(optarg, "sam") == 0) opt.flag |= MM_F_OUT_SAM;
+			if (strcmp(optarg, "sam") == 0) opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
 			else if (strcmp(optarg, "paf") == 0) opt.flag &= ~MM_F_OUT_SAM;
 			else {
 				fprintf(stderr, "[E::%s] unknown output format '%s'\n", __func__, optarg);
@@ -125,6 +126,8 @@ int main(int argc, char *argv[])
 		fprintf(stderr, "    -x STR     preset (recommended to be applied before other options) []\n");
 		fprintf(stderr, "               ava10k: -Sw5 -L100 -m0 (PacBio/ONT all-vs-all read mapping)\n");
 		fprintf(stderr, "  Input/Output:\n");
+		fprintf(stderr, "    -F STR     output format: sam or paf [paf]\n");
+		fprintf(stderr, "    -c         output CIGAR in PAF\n");
 		fprintf(stderr, "    -t INT     number of threads [%d]\n", n_threads);
 //		fprintf(stderr, "    -B NUM     process ~NUM bp in each mini-batch [100M]\n");
 //		fprintf(stderr, "    -v INT     verbose level [%d]\n", mm_verbose);
diff --git a/map.c b/map.c
index 037bc65..6200646 100644
--- a/map.c
+++ b/map.c
@@ -290,7 +290,8 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
 	regs = mm_gen_reg(qlen, n_u, u, a);
 	*n_regs = n_u;
 	mm_select_sub(opt->mask_level, opt->pri_ratio, n_regs, regs, b->km);
-	regs = mm_align_skeleton(b->km, opt, mi, qlen, seq, n_regs, regs, a);
+	if (opt->flag & MM_F_CIGAR)
+		regs = mm_align_skeleton(b->km, opt, mi, qlen, seq, n_regs, regs, a);
 
 	// free
 	kfree(b->km, a);
diff --git a/minimap.h b/minimap.h
index ec54832..06fa758 100644
--- a/minimap.h
+++ b/minimap.h
@@ -9,7 +9,8 @@
 
 #define MM_F_NO_SELF   0x01
 #define MM_F_AVA       0x02
-#define MM_F_OUT_SAM   0x04
+#define MM_F_CIGAR     0x04
+#define MM_F_OUT_SAM   0x08
 
 #define MM_IDX_MAGIC   "MMI\2"