From eccdb3a1caa2ce89477837117c7cd532179e36e4 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 1 Sep 2017 20:20:34 +0800
Subject: [PATCH] r315: added getopt from musl

---
 Makefile |   4 +-
 align.c  |   6 +-
 getopt.c | 212 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 getopt.h |  53 ++++++++++++++
 main.c   |   4 +-
 5 files changed, 273 insertions(+), 6 deletions(-)
 create mode 100644 getopt.c
 create mode 100644 getopt.h

diff --git a/Makefile b/Makefile
index f7892e8..d1ed2c0 100644
--- a/Makefile
+++ b/Makefile
@@ -21,8 +21,8 @@ all:$(PROG)
 
 extra:all $(PROG_EXTRA)
 
-minimap2:main.o libminimap2.a
-		$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
+minimap2:main.o getopt.o libminimap2.a
+		$(CC) $(CFLAGS) main.o getopt.o -o $@ -L. -lminimap2 $(LIBS)
 
 minimap2-lite:example.o libminimap2.a
 		$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
diff --git a/align.c b/align.c
index 84a7336..163a299 100644
--- a/align.c
+++ b/align.c
@@ -138,8 +138,10 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
 	if (mm_dbg_flag & MM_DBG_PRINT_ALN_SEQ) {
 		int i;
 		fprintf(stderr, "===> q=(%d,%d), e=(%d,%d), bw=%d, flag=%d, zdrop=%d <===\n", opt->q, opt->q2, opt->e, opt->e2, w, flag, opt->zdrop);
-		for (i = 0; i < tlen; ++i) fputc("ACGTN"[tseq[i]], stderr); fputc('\n', stderr);
-		for (i = 0; i < qlen; ++i) fputc("ACGTN"[qseq[i]], stderr); fputc('\n', stderr);
+		for (i = 0; i < tlen; ++i) fputc("ACGTN"[tseq[i]], stderr);
+		fputc('\n', stderr);
+		for (i = 0; i < qlen; ++i) fputc("ACGTN"[qseq[i]], stderr);
+		fputc('\n', stderr);
 	}
 	if (opt->flag & MM_F_SPLICE)
 		ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, opt->zdrop, flag, ez);
diff --git a/getopt.c b/getopt.c
new file mode 100644
index 0000000..6bb3097
--- /dev/null
+++ b/getopt.c
@@ -0,0 +1,212 @@
+#include <stddef.h>
+#include <stdio.h>
+#include <string.h>
+#include "getopt.h"
+
+char *optarg;
+int optind=1, opterr=1, optopt, __optpos, optreset=0;
+
+#define optpos __optpos
+
+static void __getopt_msg(const char *a, const char *b, const char *c, size_t l)
+{
+	FILE *f = stderr;
+	flockfile(f);
+	fputs(a, f)>=0
+	&& fwrite(b, strlen(b), 1, f)
+	&& fwrite(c, 1, l, f)==l
+	&& putc('\n', f);
+	funlockfile(f);
+}
+
+int getopt(int argc, char * const argv[], const char *optstring)
+{
+	int i, c, d;
+	int k, l;
+	char *optchar;
+
+	if (!optind || optreset) {
+		optreset = 0;
+		__optpos = 0;
+		optind = 1;
+	}
+
+	if (optind >= argc || !argv[optind])
+		return -1;
+
+	if (argv[optind][0] != '-') {
+		if (optstring[0] == '-') {
+			optarg = argv[optind++];
+			return 1;
+		}
+		return -1;
+	}
+
+	if (!argv[optind][1])
+		return -1;
+
+	if (argv[optind][1] == '-' && !argv[optind][2])
+		return optind++, -1;
+
+	if (!optpos) optpos++;
+	c = argv[optind][optpos], k = 1;
+	optchar = argv[optind]+optpos;
+	optopt = c;
+	optpos += k;
+
+	if (!argv[optind][optpos]) {
+		optind++;
+		optpos = 0;
+	}
+
+	if (optstring[0] == '-' || optstring[0] == '+')
+		optstring++;
+
+	i = 0;
+	d = 0;
+	do {
+		d = optstring[i], l = 1;
+		if (l>0) i+=l; else i++;
+	} while (l && d != c);
+
+	if (d != c) {
+		if (optstring[0] != ':' && opterr)
+			__getopt_msg(argv[0], ": unrecognized option: ", optchar, k);
+		return '?';
+	}
+	if (optstring[i] == ':') {
+		if (optstring[i+1] == ':') optarg = 0;
+		else if (optind >= argc) {
+			if (optstring[0] == ':') return ':';
+			if (opterr) __getopt_msg(argv[0],
+				": option requires an argument: ",
+				optchar, k);
+			return '?';
+		}
+		if (optstring[i+1] != ':' || optpos) {
+			optarg = argv[optind++] + optpos;
+			optpos = 0;
+		}
+	}
+	return c;
+}
+
+static void permute(char *const *argv, int dest, int src)
+{
+	char **av = (char **)argv;
+	char *tmp = av[src];
+	int i;
+	for (i=src; i>dest; i--)
+		av[i] = av[i-1];
+	av[dest] = tmp;
+}
+
+static int __getopt_long_core(int argc, char *const *argv, const char *optstring, const struct option *longopts, int *idx, int longonly)
+{
+	optarg = 0;
+	if (longopts && argv[optind][0] == '-' &&
+		((longonly && argv[optind][1] && argv[optind][1] != '-') ||
+		 (argv[optind][1] == '-' && argv[optind][2])))
+	{
+		int colon = optstring[optstring[0]=='+'||optstring[0]=='-']==':';
+		int i, cnt, match;
+		char *opt;
+		for (cnt=i=0; longopts[i].name; i++) {
+			const char *name = longopts[i].name;
+			opt = argv[optind]+1;
+			if (*opt == '-') opt++;
+			for (; *name && *name == *opt; name++, opt++);
+			if (*opt && *opt != '=') continue;
+			match = i;
+			if (!*name) {
+				cnt = 1;
+				break;
+			}
+			cnt++;
+		}
+		if (cnt==1) {
+			i = match;
+			optind++;
+			optopt = longopts[i].val;
+			if (*opt == '=') {
+				if (!longopts[i].has_arg) {
+					if (colon || !opterr)
+						return '?';
+					__getopt_msg(argv[0],
+						": option does not take an argument: ",
+						longopts[i].name,
+						strlen(longopts[i].name));
+					return '?';
+				}
+				optarg = opt+1;
+			} else if (longopts[i].has_arg == required_argument) {
+				if (!(optarg = argv[optind])) {
+					if (colon) return ':';
+					if (!opterr) return '?';
+					__getopt_msg(argv[0],
+						": option requires an argument: ",
+						longopts[i].name,
+						strlen(longopts[i].name));
+					return '?';
+				}
+				optind++;
+			}
+			if (idx) *idx = i;
+			if (longopts[i].flag) {
+				*longopts[i].flag = longopts[i].val;
+				return 0;
+			}
+			return longopts[i].val;
+		}
+		if (argv[optind][1] == '-') {
+			if (!colon && opterr)
+				__getopt_msg(argv[0], cnt ?
+					": option is ambiguous: " :
+					": unrecognized option: ",
+					argv[optind]+2,
+					strlen(argv[optind]+2));
+			optind++;
+			return '?';
+		}
+	}
+	return getopt(argc, argv, optstring);
+}
+
+static int __getopt_long(int argc, char *const *argv, const char *optstring, const struct option *longopts, int *idx, int longonly)
+{
+	int ret, skipped, resumed;
+	if (!optind || optreset) {
+		optreset = 0;
+		__optpos = 0;
+		optind = 1;
+	}
+	if (optind >= argc || !argv[optind]) return -1;
+	skipped = optind;
+	if (optstring[0] != '+' && optstring[0] != '-') {
+		int i;
+		for (i=optind; ; i++) {
+			if (i >= argc || !argv[i]) return -1;
+			if (argv[i][0] == '-' && argv[i][1]) break;
+		}
+		optind = i;
+	}
+	resumed = optind;
+	ret = __getopt_long_core(argc, argv, optstring, longopts, idx, longonly);
+	if (resumed > skipped) {
+		int i, cnt = optind-resumed;
+		for (i=0; i<cnt; i++)
+			permute(argv, skipped, optind-1);
+		optind = skipped + cnt;
+	}
+	return ret;
+}
+
+int getopt_long(int argc, char *const *argv, const char *optstring, const struct option *longopts, int *idx)
+{
+	return __getopt_long(argc, argv, optstring, longopts, idx, 0);
+}
+
+int getopt_long_only(int argc, char *const *argv, const char *optstring, const struct option *longopts, int *idx)
+{
+	return __getopt_long(argc, argv, optstring, longopts, idx, 1);
+}
diff --git a/getopt.h b/getopt.h
new file mode 100644
index 0000000..3c7bacf
--- /dev/null
+++ b/getopt.h
@@ -0,0 +1,53 @@
+/*
+  Copyright 2005-2014 Rich Felker, et al.
+  
+  Permission is hereby granted, free of charge, to any person obtaining
+  a copy of this software and associated documentation files (the
+  "Software"), to deal in the Software without restriction, including
+  without limitation the rights to use, copy, modify, merge, publish,
+  distribute, sublicense, and/or sell copies of the Software, and to
+  permit persons to whom the Software is furnished to do so, subject to
+  the following conditions:
+  
+  The above copyright notice and this permission notice shall be
+  included in all copies or substantial portions of the Software.
+  
+  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+  MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+  IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+  CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+  TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+  SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+#ifndef _GETOPT_H
+#define _GETOPT_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+int getopt(int, char * const [], const char *);
+extern char *optarg;
+extern int optind, opterr, optopt, optreset;
+
+struct option {
+	const char *name;
+	int has_arg;
+	int *flag;
+	int val;
+};
+
+int getopt_long(int, char *const *, const char *, const struct option *, int *);
+int getopt_long_only(int, char *const *, const char *, const struct option *, int *);
+
+#define no_argument        0
+#define required_argument  1
+#define optional_argument  2
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/main.c b/main.c
index 7199a07..f812451 100644
--- a/main.c
+++ b/main.c
@@ -1,4 +1,3 @@
-#include <getopt.h>
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
@@ -7,8 +6,9 @@
 #include "bseq.h"
 #include "minimap.h"
 #include "mmpriv.h"
+#include "getopt.h"
 
-#define MM_VERSION "2.1-r311"
+#define MM_VERSION "2.1-r315-dirty"
 
 void liftrlimit()
 {