From da90b614db719ea8d99591b19cb11f77e1aaf12a Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sat, 1 Jul 2017 16:54:59 -0400
Subject: [PATCH] r141: replaced -b with -a (for SAM output)

-b sounds like BAM. I like -a better.
---
 main.c     | 10 +++++-----
 minimap2.1 |  6 +++---
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/main.c b/main.c
index 25579e7..6804548 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r131-pre"
+#define MM_VERSION "2.0-r141-pre"
 
 void liftrlimit()
 {
@@ -50,7 +50,7 @@ static struct option long_options[] = {
 	{ "min-chain-score",required_argument, 0, 'm' },
 	{ "mask-level",     required_argument, 0, 'M' },
 	{ "min-dp-score",   required_argument, 0, 's' },
-	{ "sam",            no_argument,       0, 'b' },
+	{ "sam",            no_argument,       0, 'a' },
 	{ 0, 0, 0, 0}
 };
 
@@ -68,7 +68,7 @@ int main(int argc, char *argv[])
 	mm_realtime0 = realtime();
 	mm_mapopt_init(&opt);
 
-	while ((c = getopt_long(argc, argv, "bw:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:M:n:z:A:B:O:E:m:D:", long_options, &long_idx)) >= 0) {
+	while ((c = getopt_long(argc, argv, "aw:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:M:n:z:A:B:O:E:m:D:", long_options, &long_idx)) >= 0) {
 		if (c == 'w') w = atoi(optarg);
 		else if (c == 'k') k = atoi(optarg);
 		else if (c == 'H') is_hpc = 1;
@@ -83,7 +83,7 @@ int main(int argc, char *argv[])
 		else if (c == 'M') opt.mask_level = atof(optarg);
 		else if (c == 'c') opt.flag |= MM_F_CIGAR;
 		else if (c == 'S') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
-		else if (c == 'b') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
+		else if (c == 'a') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
 		else if (c == 'T') opt.sdust_thres = atoi(optarg);
 		else if (c == 'n') opt.min_cnt = atoi(optarg);
 		else if (c == 'm') opt.min_chain_score = atoi(optarg);
@@ -155,7 +155,7 @@ int main(int argc, char *argv[])
 		fprintf(stderr, "    -z INT     Z-drop score [%d]\n", opt.zdrop);
 		fprintf(stderr, "    -s INT     minimal peak DP alignment score [%d]\n", opt.min_dp_max);
 		fprintf(stderr, "  Input/Output:\n");
-		fprintf(stderr, "    -b         output in the SAM format (PAF by default)\n");
+		fprintf(stderr, "    -a         output in the SAM format (PAF by default)\n");
 		fprintf(stderr, "    -c         output CIGAR in PAF\n");
 		fprintf(stderr, "    -t INT     number of threads [%d]\n", n_threads);
 //		fprintf(stderr, "    -v INT     verbose level [%d]\n", mm_verbose);
diff --git a/minimap2.1 b/minimap2.1
index 5e95fbb..0afa761 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -1,4 +1,4 @@
-.TH minimap2 1 "30 June 2017" "minimap2-2.0-r126-pre" "Bioinformatics tools"
+.TH minimap2 1 "1 July 2017" "minimap2-2.0-r141-pre" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -28,7 +28,7 @@ minimap2
 * Long-read alignment with CIGAR:
 .RS 4
 minimap2
-.B -b
+.B -a
 .RB [ -x
 .IR preset ]
 .I target.mmi
@@ -212,7 +212,7 @@ the final CIGAR. It is the score of the max scoring segment in the alignment
 and may be different from the total alignment score.
 .SS Input/output options
 .TP 10
-.B -b
+.B -a
 Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
 by default.
 .TP