From 8b05880f73c76ccc00d2d1aa62eb3c999ca1c130 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 29 Jan 2019 10:42:20 -0500
Subject: [PATCH] r911: option -o to output to file (#319)

---
 main.c     | 14 +++++++++++---
 minimap2.1 |  7 ++++++-
 splitidx.c |  2 +-
 3 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/main.c b/main.c
index 1421959..69c45b8 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.15-r910-dirty"
+#define MM_VERSION "2.15-r911-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -99,7 +99,7 @@ static inline void yes_or_no(mm_mapopt_t *opt, int flag, int long_idx, const cha
 
 int main(int argc, char *argv[])
 {
-	const char *opt_str = "2aSDw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:yYP";
+	const char *opt_str = "2aSDw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:yYPo:";
 	ketopt_t o = KETOPT_INIT;
 	mm_mapopt_t opt;
 	mm_idxopt_t ipt;
@@ -165,6 +165,14 @@ int main(int argc, char *argv[])
 		else if (c == 'R') rg = o.arg;
 		else if (c == 'h') fp_help = stdout;
 		else if (c == '2') opt.flag |= MM_F_2_IO_THREADS;
+		else if (c == 'o') {
+			if (strcmp(o.arg, "-") != 0) {
+				if (freopen(o.arg, "wb", stdout) == NULL) {
+					fprintf(stderr, "[ERROR]\033[1;31m failed to write the output to file '%s'\033[0m\n", o.arg);
+					exit(1);
+				}
+			}
+		}
 		else if (c == 300) ipt.bucket_bits = atoi(o.arg); // --bucket-bits
 		else if (c == 302) opt.seed = atoi(o.arg); // --seed
 		else if (c == 303) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc
@@ -293,7 +301,7 @@ int main(int argc, char *argv[])
 		fprintf(fp_help, "    -u CHAR      how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]\n");
 		fprintf(fp_help, "  Input/Output:\n");
 		fprintf(fp_help, "    -a           output in the SAM format (PAF by default)\n");
-		fprintf(fp_help, "    -Q           don't output base quality in SAM\n");
+		fprintf(fp_help, "    -o FILE      output alignments to FILE [stdout]\n");
 		fprintf(fp_help, "    -L           write CIGAR with >65535 ops at the CG tag\n");
 		fprintf(fp_help, "    -R STR       SAM read group line in a format like '@RG\\tID:foo\\tSM:bar' []\n");
 		fprintf(fp_help, "    -c           output CIGAR in PAF\n");
diff --git a/minimap2.1 b/minimap2.1
index ffb8158..45ff89c 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -1,4 +1,4 @@
-.TH minimap2 1 "10 January 2019" "minimap2-2.15 (r905)" "Bioinformatics tools"
+.TH minimap2 1 "10 January 2019" "minimap2-2.15-dirty (r911)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -384,6 +384,11 @@ Set 0 to disable [0].
 Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
 by default.
 .TP
+.BI -o \ FILE
+Output alignments to
+.I FILE
+[stdout].
+.TP
 .B -Q
 Ignore base quality in the input file.
 .TP
diff --git a/splitidx.c b/splitidx.c
index 478a76e..1054a64 100644
--- a/splitidx.c
+++ b/splitidx.c
@@ -13,7 +13,7 @@ FILE *mm_split_init(const char *prefix, const mm_idx_t *mi)
 	sprintf(fn, "%s.%.4d.tmp", prefix, mi->index);
 	if ((fp = fopen(fn, "wb")) == NULL) {
 		if (mm_verbose >= 1)
-			fprintf(stderr, "[E::%s] failed to create file '%s'\n", __func__, fn);
+			fprintf(stderr, "[ERROR]\033[1;31m failed to write to temporary file '%s'\033[0m\n", fn);
 		exit(1);
 	}
 	mm_err_fwrite(&k, 4, 1, fp);