From b276772890c98fd6ec86aa91696a5ebad32c7ea0 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 18 Nov 2021 21:26:41 -0500
Subject: [PATCH] r1112: added --print-chains for debugging

---
 main.c   | 4 +++-
 map.c    | 2 +-
 mmpriv.h | 1 +
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/main.c b/main.c
index eabda3d..0329522 100644
--- a/main.c
+++ b/main.c
@@ -7,7 +7,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.23-r1111"
+#define MM_VERSION "2.23-r1112-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -76,6 +76,7 @@ static ko_longopt_t long_options[] = {
 	{ "cap-kalloc",     ko_required_argument, 349 },
 	{ "q-occ-frac",     ko_required_argument, 350 },
 	{ "chain-skip-scale",ko_required_argument,351 },
+	{ "print-chains",   ko_no_argument,       352 },
 	{ "help",           ko_no_argument,       'h' },
 	{ "max-intron-len", ko_required_argument, 'G' },
 	{ "version",        ko_no_argument,       'V' },
@@ -233,6 +234,7 @@ int main(int argc, char *argv[])
 		else if (c == 348) opt.flag |= MM_F_QSTRAND | MM_F_NO_INV; // --qstrand
 		else if (c == 349) opt.cap_kalloc = mm_parse_num(o.arg); // --cap-kalloc
 		else if (c == 350) opt.q_occ_frac = atof(o.arg); // --q-occ-frac
+		else if (c == 352) mm_dbg_flag |= MM_DBG_PRINT_CHAIN; // --print-chains
 		else if (c == 330) {
 			fprintf(stderr, "[WARNING] \033[1;31m --lj-min-ratio has been deprecated.\033[0m\n");
 		} else if (c == 314) { // --frag
diff --git a/map.c b/map.c
index 16c4716..5c31208 100644
--- a/map.c
+++ b/map.c
@@ -328,7 +328,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 		mm_hit_sort(b->km, &n_regs0, regs0, opt->alt_drop); // this step can be merged into mm_gen_regs(); will do if this shows up in profile
 	}
 
-	if (mm_dbg_flag & MM_DBG_PRINT_SEED)
+	if (mm_dbg_flag & (MM_DBG_PRINT_SEED|MM_DBG_PRINT_CHAIN))
 		for (j = 0; j < n_regs0; ++j)
 			for (i = regs0[j].as; i < regs0[j].as + regs0[j].cnt; ++i)
 				fprintf(stderr, "CN\t%d\t%s\t%d\t%c\t%d\t%d\t%d\n", j, mi->seq[a[i].x<<1>>33].name, (int32_t)a[i].x, "+-"[a[i].x>>63], (int32_t)a[i].y, (int32_t)(a[i].y>>32&0xff),
diff --git a/mmpriv.h b/mmpriv.h
index e765b47..2f5034b 100644
--- a/mmpriv.h
+++ b/mmpriv.h
@@ -13,6 +13,7 @@
 #define MM_DBG_PRINT_QNAME   0x2
 #define MM_DBG_PRINT_SEED    0x4
 #define MM_DBG_PRINT_ALN_SEQ 0x8
+#define MM_DBG_PRINT_CHAIN   0x10
 
 #define MM_SEED_LONG_JOIN  (1ULL<<40)
 #define MM_SEED_IGNORE     (1ULL<<41)