diff --git a/.gitignore b/.gitignore
index 2a8ecdc..af1bb41 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,5 @@
+.cproject
+.project
 .*.swp
 *.a
 *.o
diff --git a/Makefile b/Makefile
index f7892e8..6ed7bae 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 $(LIBS)
@@ -30,8 +30,8 @@ minimap2-lite:example.o libminimap2.a
 libminimap2.a:$(OBJS)
 		$(AR) -csru $@ $(OBJS)
 
-sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h sdust.h
-		$(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
+sdust:sdust.c getopt.o kalloc.o kalloc.h kdq.h kvec.h kseq.h sdust.h
+		$(CC) -D_SDUST_MAIN $(CFLAGS) $< getopt.o kalloc.o -o $@ -lz
 
 clean:
 		rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM session*
@@ -46,6 +46,7 @@ bseq.o: bseq.h kseq.h
 chain.o: minimap.h mmpriv.h bseq.h kalloc.h
 example.o: minimap.h kseq.h
 format.o: kalloc.h mmpriv.h minimap.h bseq.h
+getopt.o: getopt.h
 hit.o: mmpriv.h minimap.h bseq.h kalloc.h
 index.o: kthread.h bseq.h minimap.h mmpriv.h kvec.h kalloc.h khash.h
 kalloc.o: kalloc.h
@@ -53,7 +54,7 @@ ksw2_extd2_sse.o: ksw2.h kalloc.h
 ksw2_exts2_sse.o: ksw2.h kalloc.h
 ksw2_extz2_sse.o: ksw2.h kalloc.h
 ksw2_ll_sse.o: ksw2.h kalloc.h
-main.o: bseq.h minimap.h mmpriv.h
+main.o: bseq.h minimap.h mmpriv.h getopt.h
 map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h
 misc.o: minimap.h ksort.h
 sdust.o: kalloc.h kdq.h kvec.h sdust.h
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/example.c b/example.c
index ca9da09..ccb1e68 100644
--- a/example.c
+++ b/example.c
@@ -35,13 +35,13 @@ int main(int argc, char *argv[])
 	opt.flag |= MM_F_CIGAR; // perform alignment
 	mm_tbuf_t *tbuf = mm_tbuf_init(); // thread buffer; for multi-threading, allocate one tbuf for each thread
 	while (kseq_read(ks) >= 0) { // each kseq_read() call reads one query sequence
-		const mm_reg1_t *reg;
+		mm_reg1_t *reg;
 		int j, i, n_reg;
 		// get all hits for the query
 		reg = mm_map(mi, ks->seq.l, ks->seq.s, &n_reg, tbuf, &opt, 0);
 		// traverse hits and print them out
 		for (j = 0; j < n_reg; ++j) {
-			const mm_reg1_t *r = &reg[j];
+			mm_reg1_t *r = &reg[j];
 			assert(r->p); // with MM_F_CIGAR, this should not be NULL
 			printf("%s\t%d\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]);
 			printf("%s\t%d\t%d\t%d\t%d\t%d\t%d\tcg:Z:", mi->seq[r->rid].name, mi->seq[r->rid].len, r->rs, r->re,
@@ -49,7 +49,9 @@ int main(int argc, char *argv[])
 			for (i = 0; i < r->p->n_cigar; ++i) // IMPORTANT: this gives the CIGAR in the aligned regions. NO soft/hard clippings!
 				printf("%d%c", r->p->cigar[i]>>4, "MIDSHN"[r->p->cigar[i]&0xf]);
 			putchar('\n');
+			free(r->p);
 		}
+		free(reg);
 	}
 	mm_tbuf_destroy(tbuf);
 
diff --git a/getopt.c b/getopt.c
new file mode 100644
index 0000000..7139bfd
--- /dev/null
+++ b/getopt.c
@@ -0,0 +1,216 @@
+#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;
+#if !defined(WIN32) && !defined(_WIN32)
+	flockfile(f);
+#endif
+	fputs(a, f);
+	fwrite(b, strlen(b), 1, f);
+	fwrite(c, 1, l, f);
+	fputc('\n', f);
+#if !defined(WIN32) && !defined(_WIN32)
+	funlockfile(f);
+#endif
+}
+
+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/index.c b/index.c
index dc58231..2123ab5 100644
--- a/index.c
+++ b/index.c
@@ -1,6 +1,10 @@
 #include <stdlib.h>
 #include <assert.h>
+#if defined(WIN32) || defined(_WIN32)
+#include <io.h> // for open(2)
+#else
 #include <unistd.h>
+#endif
 #include <fcntl.h>
 #include <stdio.h>
 #include "kthread.h"
diff --git a/kalloc.c b/kalloc.c
index 9356d40..fa9bc88 100644
--- a/kalloc.c
+++ b/kalloc.c
@@ -46,7 +46,7 @@ static size_t *morecore(kmem_t *km, size_t nu)
 	up = (size_t*)malloc(rnu * sizeof(size_t));
 	if (!up) { /* fail to allocate memory */
 		km_stat(km);
-		fprintf(stderr, "[morecore] %lu bytes requested but not available.\n", rnu * sizeof(size_t));
+		fprintf(stderr, "[morecore] %lu bytes requested but not available.\n", (unsigned long)rnu * sizeof(size_t));
 		exit(1);
 	}
 	/* put the pointer in km->list_head */
@@ -210,5 +210,5 @@ void km_stat(const void *_km)
 	--n_blocks;
 	frag = 1.0/1024.0 * n_units * sizeof(size_t) / n_blocks;
 	fprintf(stderr, "[kr_stat] tot=%lu, free=%lu, n_block=%u, max_block=%lu, frag_len=%.3fK\n",
-			km->total_allocated, n_units * sizeof(size_t), n_blocks, max_block * sizeof(size_t), frag);
+			(unsigned long)km->total_allocated, (unsigned long)n_units * sizeof(size_t), n_blocks, (unsigned long)max_block * sizeof(size_t), frag);
 }
diff --git a/kdq.h b/kdq.h
index 4a67c0b..8ae5c97 100644
--- a/kdq.h
+++ b/kdq.h
@@ -3,11 +3,12 @@
 
 #include <stdlib.h>
 #include <string.h>
+#include <stdint.h>
 #include "kalloc.h"
 
 #define __KDQ_TYPE(type) \
 	typedef struct { \
-		size_t front:58, bits:6, count, mask; \
+		uint64_t front:58, bits:6, count, mask; \
 		type *a; \
 		void *km; \
 	} kdq_##type##_t;
diff --git a/ksort.h b/ksort.h
index 1f2a3dd..7cd65a5 100644
--- a/ksort.h
+++ b/ksort.h
@@ -30,6 +30,7 @@
 
 #include <stdlib.h>
 #include <string.h>
+#include <assert.h>
 
 typedef struct {
 	void *left, *right;
@@ -78,6 +79,7 @@ typedef const char *ksstr_t;
 #define KSORT_INIT_STR KSORT_INIT(str, ksstr_t, ks_lt_str)
 
 #define RS_MIN_SIZE 64
+#define RS_MAX_BITS 8
 
 #define KRADIX_SORT_INIT(name, rstype_t, rskey, sizeof_key) \
 	typedef struct { \
@@ -98,7 +100,8 @@ typedef const char *ksstr_t;
 	{ \
 		rstype_t *i; \
 		int size = 1<<n_bits, m = size - 1; \
-		rsbucket_##name##_t *k, b[size], *be = b + size; \
+		rsbucket_##name##_t *k, b[1<<RS_MAX_BITS], *be = b + size; \
+		assert(n_bits <= RS_MAX_BITS); \
 		for (k = b; k != be; ++k) k->b = k->e = beg; \
 		for (i = beg; i != end; ++i) ++b[rskey(*i)>>s&m].e; \
 		for (k = b + 1; k != be; ++k) \
@@ -127,7 +130,7 @@ typedef const char *ksstr_t;
 	void radix_sort_##name(rstype_t *beg, rstype_t *end) \
 	{ \
 		if (end - beg <= RS_MIN_SIZE) rs_insertsort_##name(beg, end); \
-		else rs_sort_##name(beg, end, 8, sizeof_key * 8 - 8); \
+		else rs_sort_##name(beg, end, RS_MAX_BITS, (sizeof_key - 1) * RS_MAX_BITS); \
 	}
 
 #endif
diff --git a/kthread.c b/kthread.c
index f991714..249ceea 100644
--- a/kthread.c
+++ b/kthread.c
@@ -1,6 +1,11 @@
 #include <pthread.h>
 #include <stdlib.h>
 #include <limits.h>
+#include <stdint.h>
+
+#if (defined(WIN32) || defined(_WIN32)) && defined(_MSC_VER)
+#define __sync_fetch_and_add(ptr, addend)     _InterlockedExchangeAdd((void*)ptr, addend)
+#endif
 
 /************
  * kt_for() *
@@ -52,12 +57,13 @@ void kt_for(int n_threads, void (*func)(void*,long,int), void *data, long n)
 		kt_for_t t;
 		pthread_t *tid;
 		t.func = func, t.data = data, t.n_threads = n_threads, t.n = n;
-		t.w = (ktf_worker_t*)alloca(n_threads * sizeof(ktf_worker_t));
-		tid = (pthread_t*)alloca(n_threads * sizeof(pthread_t));
+		t.w = (ktf_worker_t*)calloc(n_threads, sizeof(ktf_worker_t));
+		tid = (pthread_t*)calloc(n_threads, sizeof(pthread_t));
 		for (i = 0; i < n_threads; ++i)
 			t.w[i].t = &t, t.w[i].i = i;
 		for (i = 0; i < n_threads; ++i) pthread_create(&tid[i], 0, ktf_worker, &t.w[i]);
 		for (i = 0; i < n_threads; ++i) pthread_join(tid[i], 0);
+		free(tid); free(t.w);
 	} else {
 		long j;
 		for (j = 0; j < n; ++j) func(data, j, 0);
@@ -135,16 +141,17 @@ void kt_pipeline(int n_threads, void *(*func)(void*, int, void*), void *shared_d
 	pthread_mutex_init(&aux.mutex, 0);
 	pthread_cond_init(&aux.cv, 0);
 
-	aux.workers = (ktp_worker_t*)alloca(n_threads * sizeof(ktp_worker_t));
+	aux.workers = (ktp_worker_t*)calloc(n_threads, sizeof(ktp_worker_t));
 	for (i = 0; i < n_threads; ++i) {
 		ktp_worker_t *w = &aux.workers[i];
 		w->step = 0; w->pl = &aux; w->data = 0;
 		w->index = aux.index++;
 	}
 
-	tid = (pthread_t*)alloca(n_threads * sizeof(pthread_t));
+	tid = (pthread_t*)calloc(n_threads, sizeof(pthread_t));
 	for (i = 0; i < n_threads; ++i) pthread_create(&tid[i], 0, ktp_worker, &aux.workers[i]);
 	for (i = 0; i < n_threads; ++i) pthread_join(tid[i], 0);
+	free(tid); free(aux.workers);
 
 	pthread_mutex_destroy(&aux.mutex);
 	pthread_cond_destroy(&aux.cv);
diff --git a/main.c b/main.c
index d67b61c..b99fa5d 100644
--- a/main.c
+++ b/main.c
@@ -1,24 +1,26 @@
-#include <getopt.h>
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
-#include <sys/resource.h>
-#include <sys/time.h>
 #include "bseq.h"
 #include "minimap.h"
 #include "mmpriv.h"
+#include "getopt.h"
 
-#define MM_VERSION "2.1-r311"
+#define MM_VERSION "2.1-r335-dirty"
 
+#ifdef __linux__
+#include <sys/resource.h>
+#include <sys/time.h>
 void liftrlimit()
 {
-#ifdef __linux__
 	struct rlimit r;
 	getrlimit(RLIMIT_AS, &r);
 	r.rlim_cur = r.rlim_max;
 	setrlimit(RLIMIT_AS, &r);
-#endif
 }
+#else
+void liftrlimit() {}
+#endif
 
 static struct option long_options[] = {
 	{ "bucket-bits",    required_argument, 0, 0 },
@@ -250,6 +252,7 @@ int main(int argc, char *argv[])
 		mm_idx_t *mi;
 		if (fpr) {
 			mi = mm_idx_load(fpr);
+			if (mi == 0) break;
 			if (idx_par_set && mm_verbose >= 2 && (mi->k != k || mi->w != w || mi->is_hpc != is_hpc))
 				fprintf(stderr, "[WARNING] \033[1;31mIndexing parameters on the command line (-k/-w/-H) overridden by parameters in the prebuilt index.\033[0m\n");
 		} else {
diff --git a/map.c b/map.c
index f531efa..14366ad 100644
--- a/map.c
+++ b/map.c
@@ -382,7 +382,11 @@ int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int
 	pipeline_t pl;
 	memset(&pl, 0, sizeof(pipeline_t));
 	pl.fp = mm_bseq_open(fn);
-	if (pl.fp == 0) return -1;
+	if (pl.fp == 0) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "ERROR: failed to open file '%s'\n", fn);
+		return -1;
+	}
 	pl.opt = opt, pl.mi = idx;
 	pl.n_threads = n_threads, pl.mini_batch_size = mini_batch_size;
 	if ((opt->flag & MM_F_OUT_SAM) && !(opt->flag & MM_F_NO_SAM_SQ))
diff --git a/misc.c b/misc.c
index f6699ed..d7dd1e4 100644
--- a/misc.c
+++ b/misc.c
@@ -1,17 +1,102 @@
-#include <sys/resource.h>
-#include <sys/time.h>
 #include "minimap.h"
 
 int mm_verbose = 3;
 int mm_dbg_flag = 0;
 double mm_realtime0;
 
+#if defined(WIN32) || defined(_WIN32)
+#include <windows.h>
+
+struct timezone
+{
+  __int32  tz_minuteswest; /* minutes W of Greenwich */
+  int  tz_dsttime;     /* type of dst correction */
+};
+
+/*
+ * gettimeofday.c
+ *    Win32 gettimeofday() replacement
+ *    taken from PostgreSQL, according to
+ *    https://stackoverflow.com/questions/1676036/what-should-i-use-to-replace-gettimeofday-on-windows
+ *
+ * src/port/gettimeofday.c
+ *
+ * Copyright (c) 2003 SRA, Inc.
+ * Copyright (c) 2003 SKC, Inc.
+ *
+ * Permission to use, copy, modify, and distribute this software and
+ * its documentation for any purpose, without fee, and without a
+ * written agreement is hereby granted, provided that the above
+ * copyright notice and this paragraph and the following two
+ * paragraphs appear in all copies.
+ *
+ * IN NO EVENT SHALL THE AUTHOR BE LIABLE TO ANY PARTY FOR DIRECT,
+ * INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING
+ * LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS
+ * DOCUMENTATION, EVEN IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED
+ * OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ * THE AUTHOR SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ * A PARTICULAR PURPOSE.  THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS
+ * IS" BASIS, AND THE AUTHOR HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE,
+ * SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
+ */
+
+/* FILETIME of Jan 1 1970 00:00:00. */
+static const unsigned __int64 epoch = ((unsigned __int64) 116444736000000000ULL);
+
+/*
+ * timezone information is stored outside the kernel so tzp isn't used anymore.
+ *
+ * Note: this function is not for Win32 high precision timing purpose. See
+ * elapsed_time().
+ */
+int gettimeofday(struct timeval * tp, struct timezone *tzp)
+{
+    FILETIME    file_time;
+    SYSTEMTIME  system_time;
+    ULARGE_INTEGER ularge;
+
+    GetSystemTime(&system_time);
+    SystemTimeToFileTime(&system_time, &file_time);
+    ularge.LowPart = file_time.dwLowDateTime;
+    ularge.HighPart = file_time.dwHighDateTime;
+
+    tp->tv_sec = (long) ((ularge.QuadPart - epoch) / 10000000L);
+    tp->tv_usec = (long) (system_time.wMilliseconds * 1000);
+
+    return 0;
+}
+
+// taken from https://stackoverflow.com/questions/5272470/c-get-cpu-usage-on-linux-and-windows
+double cputime()
+{
+	HANDLE hProcess = GetCurrentProcess();
+	FILETIME ftCreation, ftExit, ftKernel, ftUser;
+	SYSTEMTIME stKernel;
+	SYSTEMTIME stUser;
+
+	GetProcessTimes(hProcess, &ftCreation, &ftExit, &ftKernel, &ftUser);
+	FileTimeToSystemTime(&ftKernel, &stKernel);
+	FileTimeToSystemTime(&ftUser, &stUser);
+
+	double kernelModeTime = ((stKernel.wHour * 60.) + stKernel.wMinute * 60.) + stKernel.wSecond * 1. + stKernel.wMilliseconds / 1000.;
+	double userModeTime = ((stUser.wHour * 60.) + stUser.wMinute * 60.) + stUser.wSecond * 1. + stUser.wMilliseconds / 1000.;
+
+	return kernelModeTime + userModeTime;
+}
+#else
+#include <sys/resource.h>
+#include <sys/time.h>
+
 double cputime()
 {
 	struct rusage r;
 	getrusage(RUSAGE_SELF, &r);
 	return r.ru_utime.tv_sec + r.ru_stime.tv_sec + 1e-6 * (r.ru_utime.tv_usec + r.ru_stime.tv_usec);
 }
+#endif /* WIN32 || _WIN32 */
 
 double realtime()
 {
diff --git a/sdust.c b/sdust.c
index 07339dd..f1e47e8 100644
--- a/sdust.c
+++ b/sdust.c
@@ -176,7 +176,7 @@ uint64_t *sdust(void *km, const uint8_t *seq, int l_seq, int T, int W, int *n)
 #ifdef _SDUST_MAIN
 #include <zlib.h>
 #include <stdio.h>
-#include <unistd.h>
+#include "getopt.h"
 #include "kseq.h"
 KSEQ_INIT(gzFile, gzread)
 
diff --git a/sketch.c b/sketch.c
index b141cba..db359eb 100644
--- a/sketch.c
+++ b/sketch.c
@@ -77,11 +77,10 @@ void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, i
 {
 	uint64_t shift1 = 2 * (k - 1), mask = (1ULL<<2*k) - 1, kmer[2] = {0,0};
 	int i, j, l, buf_pos, min_pos, kmer_span = 0;
-	mm128_t *buf, min = { UINT64_MAX, UINT64_MAX };
+	mm128_t buf[256], min = { UINT64_MAX, UINT64_MAX };
 	tiny_queue_t tq;
 
-	assert(len > 0 && w > 0 && k > 0 && k <= 28); // 56 bits for k-mer; could use long k-mers, but 28 enough in practice
-	buf = (mm128_t*)alloca(w * 16);
+	assert(len > 0 && (w > 0 && w < 256) && (k > 0 && k <= 28)); // 56 bits for k-mer; could use long k-mers, but 28 enough in practice
 	memset(buf, 0xff, w * 16);
 	memset(&tq, 0, sizeof(tiny_queue_t));
 	kv_resize(mm128_t, km, *p, p->n + len/w);