From c8f0a35c4078f2430712da8c4ad4e3a696fe51f0 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Wed, 24 Nov 2021 16:49:48 -0500
Subject: [PATCH] r1117: added --no-hash-name for deterministic

---
 main.c     | 4 +++-
 map.c      | 2 +-
 minimap.h  | 1 +
 minimap2.1 | 3 +++
 4 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/main.c b/main.c
index 67d6a29..900bd08 100644
--- a/main.c
+++ b/main.c
@@ -7,7 +7,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.23-r1116-dirty"
+#define MM_VERSION "2.23-r1117-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -77,6 +77,7 @@ static ko_longopt_t long_options[] = {
 	{ "q-occ-frac",     ko_required_argument, 350 },
 	{ "chain-skip-scale",ko_required_argument,351 },
 	{ "print-chains",   ko_no_argument,       352 },
+	{ "no-hash-name",   ko_no_argument,       353 },
 	{ "help",           ko_no_argument,       'h' },
 	{ "max-intron-len", ko_required_argument, 'G' },
 	{ "version",        ko_no_argument,       'V' },
@@ -235,6 +236,7 @@ int main(int argc, char *argv[])
 		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 == 353) opt.flag |= MM_F_NO_HASH_NAME; // --no-hash-name
 		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 5c31208..5311468 100644
--- a/map.c
+++ b/map.c
@@ -248,7 +248,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 	if (qlen_sum == 0 || n_segs <= 0 || n_segs > MM_MAX_SEG) return;
 	if (opt->max_qlen > 0 && qlen_sum > opt->max_qlen) return;
 
-	hash  = qname? __ac_X31_hash_string(qname) : 0;
+	hash  = qname && !(opt->flag & MM_F_NO_HASH_NAME)? __ac_X31_hash_string(qname) : 0;
 	hash ^= __ac_Wang_hash(qlen_sum) + __ac_Wang_hash(opt->seed);
 	hash  = __ac_Wang_hash(hash);
 
diff --git a/minimap.h b/minimap.h
index 5a0ff2f..13e12e0 100644
--- a/minimap.h
+++ b/minimap.h
@@ -39,6 +39,7 @@
 #define MM_F_RMQ           (0x80000000LL)
 #define MM_F_QSTRAND       (0x100000000LL)
 #define MM_F_NO_INV        (0x200000000LL)
+#define MM_F_NO_HASH_NAME  (0x400000000LL)
 
 #define MM_I_HPC          0x1
 #define MM_I_NO_SEQ       0x2
diff --git a/minimap2.1 b/minimap2.1
index c321e60..7d0c2c5 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -318,6 +318,9 @@ faster for short reads, but slower for long reads. [no]
 .B --no-pairing
 Treat two reads in a pair as independent reads. The mate related fields in SAM
 are still properly populated.
+.TP
+.B --no-hash-name
+Produce the same alignment for identical sequences regardless of their sequence names.
 .SS Alignment options
 .TP 10
 .BI -A \ INT