From ae2adf04d4d73c59898ac8c7f01f2f68773176b0 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 5 Oct 2017 15:39:26 -0400
Subject: [PATCH] r476: multi-file fragment mode working

---
 main.c     | 13 ++++++++-----
 map.c      |  1 +
 minimap.h  |  2 ++
 minimap2.1 |  2 +-
 4 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/main.c b/main.c
index 9088a29..197653d 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.2-r475-dirty"
+#define MM_VERSION "2.2-r476-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -37,7 +37,7 @@ static struct option long_options[] = {
 	{ "cost-non-gt-ag", required_argument, 0, 0 },
 	{ "no-long-join",   no_argument,       0, 0 },
 	{ "sr",             no_argument,       0, 0 },
-	{ "multi",          optional_argument, 0, 0 },
+	{ "frag",           optional_argument, 0, 0 },
 	{ "print-2nd",      optional_argument, 0, 0 },
 	{ "cs",             optional_argument, 0, 0 },
 	{ "help",           no_argument,       0, 'h' },
@@ -129,7 +129,7 @@ int main(int argc, char *argv[])
 		else if (c == 0 && long_idx ==11) opt.noncan = atoi(optarg); // --cost-non-gt-ag
 		else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
 		else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
-		else if (c == 0 && long_idx == 14) { // --multi
+		else if (c == 0 && long_idx == 14) { // --frag
 			if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
 				opt.flag |= MM_F_MULTI_SEG;
 			else opt.flag &= ~MM_F_MULTI_SEG;
@@ -267,8 +267,11 @@ int main(int argc, char *argv[])
 					__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), mi->n_seq);
 		if (argc != optind + 1) mm_mapopt_update(&opt, mi);
 		if (mm_verbose >= 3) mm_idx_stat(mi);
-		for (i = optind + 1; i < argc; ++i)
-			mm_map_file(mi, argv[i], &opt, n_threads);
+		if (opt.flag & MM_F_MULTI_SEG)
+			mm_map_file_multi_seg(mi, argc - (optind + 1), (const char**)&argv[optind + 1], &opt, n_threads);
+		else
+			for (i = optind + 1; i < argc; ++i)
+				mm_map_file(mi, argv[i], &opt, n_threads);
 		mm_idx_destroy(mi);
 	}
 	mm_idx_reader_close(idx_rdr);
diff --git a/map.c b/map.c
index a8a1ed0..595214d 100644
--- a/map.c
+++ b/map.c
@@ -490,6 +490,7 @@ int mm_map_file_multi_seg(const mm_idx_t *idx, int n_segs, const char **fn, cons
 	pipeline_t pl;
 	if (n_segs < 1) return -1;
 	memset(&pl, 0, sizeof(pipeline_t));
+	pl.n_fp = n_segs;
 	pl.fp = (mm_bseq_file_t**)calloc(n_segs, sizeof(mm_bseq_file_t*));
 	for (i = 0; i < n_segs; ++i) {
 		pl.fp[i] = mm_bseq_open(fn[i]);
diff --git a/minimap.h b/minimap.h
index aa7a098..eb11282 100644
--- a/minimap.h
+++ b/minimap.h
@@ -258,6 +258,8 @@ mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, m
  */
 int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int n_threads);
 
+int mm_map_file_multi_seg(const mm_idx_t *idx, int n_segs, const char **fn, const mm_mapopt_t *opt, int n_threads);
+
 // deprecated APIs for backward compatibility
 void mm_mapopt_init(mm_mapopt_t *opt);
 mm_idx_t *mm_idx_build(const char *fn, int w, int k, int is_hpc, int n_threads);
diff --git a/minimap2.1 b/minimap2.1
index 4cea3f7..b914413 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -348,7 +348,7 @@ tag ignores introns to demote hits to pseudogenes.
 Short single-end reads without splicing
 .RB ( -k21
 .B -w11 -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200
-.B -K50m --multi
+.B -K50m --frag
 .BR --sr ).
 .RE
 .SS Miscellaneous options