From 53c4bf5e4fd9fc9d36052a8be4c679c15b34dbfe Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 3 Jul 2017 11:02:32 -0400
Subject: [PATCH] r149: introduced debugging flags on CLI

---
 main.c    | 10 +++++++---
 map.c     |  5 +++--
 minimap.h |  2 +-
 misc.c    |  1 +
 mmpriv.h  |  3 +++
 5 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/main.c b/main.c
index 569319f..a0115ad 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r148-pre"
+#define MM_VERSION "2.0-r149-pre"
 
 void liftrlimit()
 {
@@ -45,6 +45,8 @@ static struct option long_options[] = {
 	{ "bucket-bits",    required_argument, 0, 0 },
 	{ "mb-size",        required_argument, 0, 0 },
 	{ "int-rname",      no_argument,       0, 0 },
+	{ "no-kalloc",      no_argument,       0, 0 },
+	{ "print-qname",    no_argument,       0, 0 },
 	{ "version",        no_argument,       0, 'V' },
 	{ "min-count",      required_argument, 0, 'n' },
 	{ "min-chain-score",required_argument, 0, 'm' },
@@ -94,8 +96,10 @@ int main(int argc, char *argv[])
 		else if (c == 'E') opt.e = atoi(optarg);
 		else if (c == 'z') opt.zdrop = atoi(optarg);
 		else if (c == 's') opt.min_dp_max = atoi(optarg);
-		else if (c == 0 && long_idx == 0) bucket_bits = atoi(optarg); // bucket-bits
-		else if (c == 0 && long_idx == 2) keep_name = 0; // int-rname
+		else if (c == 0 && long_idx == 0) bucket_bits = atoi(optarg); // --bucket-bits
+		else if (c == 0 && long_idx == 2) keep_name = 0; // --int-rname
+		else if (c == 0 && long_idx == 3) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc
+		else if (c == 0 && long_idx == 4) mm_dbg_flag |= MM_DBG_PRINT_QNAME; // --print-qname
 		else if (c == 'V') {
 			puts(MM_VERSION);
 			return 0;
diff --git a/map.c b/map.c
index c36698d..9f18cc7 100644
--- a/map.c
+++ b/map.c
@@ -64,7 +64,7 @@ mm_tbuf_t *mm_tbuf_init(void)
 {
 	mm_tbuf_t *b;
 	b = (mm_tbuf_t*)calloc(1, sizeof(mm_tbuf_t));
-	if (mm_verbose < 10) b->km = km_init();
+	if (!(mm_dbg_flag & 1)) b->km = km_init();
 	b->sdb = sdust_buf_init(b->km);
 	return b;
 }
@@ -262,7 +262,6 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
 mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
 {
 	mm_reg1_t *regs;
-	if (mm_verbose >= 11) fprintf(stderr, "===> %s <===\n", qname);
 	b->mini.n = 0;
 	mm_sketch(b->km, seq, l_seq, mi->w, mi->k, 0, mi->is_hpc, &b->mini);
 	if (opt->sdust_thres > 0)
@@ -295,6 +294,8 @@ typedef struct {
 static void worker_for(void *_data, long i, int tid) // kt_for() callback
 {
     step_t *step = (step_t*)_data;
+	if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
+		fprintf(stderr, "Processing query %s on thread %d\n", step->seq[i].name, tid);
 	step->reg[i] = mm_map(step->p->mi, step->seq[i].l_seq, step->seq[i].seq, &step->n_reg[i], step->buf[tid], step->p->opt, step->seq[i].name);
 }
 
diff --git a/minimap.h b/minimap.h
index 496fe87..fc3f4fc 100644
--- a/minimap.h
+++ b/minimap.h
@@ -93,7 +93,7 @@ typedef struct {
 	int mid_occ;
 } mm_mapopt_t;
 
-extern int mm_verbose;
+extern int mm_verbose, mm_dbg_flag;
 extern double mm_realtime0;
 
 struct mm_tbuf_s;
diff --git a/misc.c b/misc.c
index 9a85fec..f6699ed 100644
--- a/misc.c
+++ b/misc.c
@@ -3,6 +3,7 @@
 #include "minimap.h"
 
 int mm_verbose = 3;
+int mm_dbg_flag = 0;
 double mm_realtime0;
 
 double cputime()
diff --git a/mmpriv.h b/mmpriv.h
index 46e216e..6f7c48d 100644
--- a/mmpriv.h
+++ b/mmpriv.h
@@ -8,6 +8,9 @@
 #define MM_PARENT_UNSET   (-1)
 #define MM_PARENT_TMP_PRI (-2)
 
+#define MM_DBG_NO_KALLOC   0x1
+#define MM_DBG_PRINT_QNAME 0x2
+
 #ifndef kroundup32
 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
 #endif