minimap2 0.2.22.0 → 0.2.24.1

data/ext/minimap2/index.c

@@ -0,0 +1,775 @@
+#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>
+#define __STDC_LIMIT_MACROS
+#include "kthread.h"
+#include "bseq.h"
+#include "minimap.h"
+#include "mmpriv.h"
+#include "kvec.h"
+#include "khash.h"
+
+#define idx_hash(a) ((a)>>1)
+#define idx_eq(a, b) ((a)>>1 == (b)>>1)
+KHASH_INIT(idx, uint64_t, uint64_t, 1, idx_hash, idx_eq)
+typedef khash_t(idx) idxhash_t;
+
+KHASH_MAP_INIT_STR(str, uint32_t)
+
+#define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x))
+
+typedef struct mm_idx_bucket_s {
+	mm128_v a;   // (minimizer, position) array
+	int32_t n;   // size of the _p_ array
+	uint64_t *p; // position array for minimizers appearing >1 times
+	void *h;     // hash table indexing _p_ and minimizers appearing once
+} mm_idx_bucket_t;
+
+typedef struct {
+	int32_t st, en, max; // max is not used for now
+	int32_t score:30, strand:2;
+} mm_idx_intv1_t;
+
+typedef struct mm_idx_intv_s {
+	int32_t n, m;
+	mm_idx_intv1_t *a;
+} mm_idx_intv_t;
+
+mm_idx_t *mm_idx_init(int w, int k, int b, int flag)
+{
+	mm_idx_t *mi;
+	if (k*2 < b) b = k * 2;
+	if (w < 1) w = 1;
+	mi = (mm_idx_t*)calloc(1, sizeof(mm_idx_t));
+	mi->w = w, mi->k = k, mi->b = b, mi->flag = flag;
+	mi->B = (mm_idx_bucket_t*)calloc(1<<b, sizeof(mm_idx_bucket_t));
+	if (!(mm_dbg_flag & 1)) mi->km = km_init();
+	return mi;
+}
+
+void mm_idx_destroy(mm_idx_t *mi)
+{
+	uint32_t i;
+	if (mi == 0) return;
+	if (mi->h) kh_destroy(str, (khash_t(str)*)mi->h);
+	if (mi->B) {
+		for (i = 0; i < 1U<<mi->b; ++i) {
+			free(mi->B[i].p);
+			free(mi->B[i].a.a);
+			kh_destroy(idx, (idxhash_t*)mi->B[i].h);
+		}
+	}
+	if (mi->I) {
+		for (i = 0; i < mi->n_seq; ++i)
+			free(mi->I[i].a);
+		free(mi->I);
+	}
+	if (!mi->km) {
+		for (i = 0; i < mi->n_seq; ++i)
+			free(mi->seq[i].name);
+		free(mi->seq);
+	} else km_destroy(mi->km);
+	free(mi->B); free(mi->S); free(mi);
+}
+
+const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n)
+{
+	int mask = (1<<mi->b) - 1;
+	khint_t k;
+	mm_idx_bucket_t *b = &mi->B[minier&mask];
+	idxhash_t *h = (idxhash_t*)b->h;
+	*n = 0;
+	if (h == 0) return 0;
+	k = kh_get(idx, h, minier>>mi->b<<1);
+	if (k == kh_end(h)) return 0;
+	if (kh_key(h, k)&1) { // special casing when there is only one k-mer
+		*n = 1;
+		return &kh_val(h, k);
+	} else {
+		*n = (uint32_t)kh_val(h, k);
+		return &b->p[kh_val(h, k)>>32];
+	}
+}
+
+void mm_idx_stat(const mm_idx_t *mi)
+{
+	int n = 0, n1 = 0;
+	uint32_t i;
+	uint64_t sum = 0, len = 0;
+	fprintf(stderr, "[M::%s] kmer size: %d; skip: %d; is_hpc: %d; #seq: %d\n", __func__, mi->k, mi->w, mi->flag&MM_I_HPC, mi->n_seq);
+	for (i = 0; i < mi->n_seq; ++i)
+		len += mi->seq[i].len;
+	for (i = 0; i < 1U<<mi->b; ++i)
+		if (mi->B[i].h) n += kh_size((idxhash_t*)mi->B[i].h);
+	for (i = 0; i < 1U<<mi->b; ++i) {
+		idxhash_t *h = (idxhash_t*)mi->B[i].h;
+		khint_t k;
+		if (h == 0) continue;
+		for (k = 0; k < kh_end(h); ++k)
+			if (kh_exist(h, k)) {
+				sum += kh_key(h, k)&1? 1 : (uint32_t)kh_val(h, k);
+				if (kh_key(h, k)&1) ++n1;
+			}
+	}
+	fprintf(stderr, "[M::%s::%.3f*%.2f] distinct minimizers: %d (%.2f%% are singletons); average occurrences: %.3lf; average spacing: %.3lf; total length: %ld\n",
+			__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), n, 100.0*n1/n, (double)sum / n, (double)len / sum, (long)len);
+}
+
+int mm_idx_index_name(mm_idx_t *mi)
+{
+	khash_t(str) *h;
+	uint32_t i;
+	int has_dup = 0, absent;
+	if (mi->h) return 0;
+	h = kh_init(str);
+	for (i = 0; i < mi->n_seq; ++i) {
+		khint_t k;
+		k = kh_put(str, h, mi->seq[i].name, &absent);
+		if (absent) kh_val(h, k) = i;
+		else has_dup = 1;
+	}
+	mi->h = h;
+	if (has_dup && mm_verbose >= 2)
+		fprintf(stderr, "[WARNING] some database sequences have identical sequence names\n");
+	return has_dup;
+}
+
+int mm_idx_name2id(const mm_idx_t *mi, const char *name)
+{
+	khash_t(str) *h = (khash_t(str)*)mi->h;
+	khint_t k;
+	if (h == 0) return -2;
+	k = kh_get(str, h, name);
+	return k == kh_end(h)? -1 : kh_val(h, k);
+}
+
+int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq)
+{
+	uint64_t i, st1, en1;
+	if (rid >= mi->n_seq || st >= mi->seq[rid].len) return -1;
+	if (en > mi->seq[rid].len) en = mi->seq[rid].len;
+	st1 = mi->seq[rid].offset + st;
+	en1 = mi->seq[rid].offset + en;
+	for (i = st1; i < en1; ++i)
+		seq[i - st1] = mm_seq4_get(mi->S, i);
+	return en - st;
+}
+
+int mm_idx_getseq_rev(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq)
+{
+	uint64_t i, st1, en1;
+	const mm_idx_seq_t *s;
+	if (rid >= mi->n_seq || st >= mi->seq[rid].len) return -1;
+	s = &mi->seq[rid];
+	if (en > s->len) en = s->len;
+	st1 = s->offset + (s->len - en);
+	en1 = s->offset + (s->len - st);
+	for (i = st1; i < en1; ++i) {
+		uint8_t c = mm_seq4_get(mi->S, i);
+		seq[en1 - i - 1] = c < 4? 3 - c : c;
+	}
+	return en - st;
+}
+
+int mm_idx_getseq2(const mm_idx_t *mi, int is_rev, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq)
+{
+	if (is_rev) return mm_idx_getseq_rev(mi, rid, st, en, seq);
+	else return mm_idx_getseq(mi, rid, st, en, seq);
+}
+
+int32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f)
+{
+	int i;
+	size_t n = 0;
+	uint32_t thres;
+	khint_t *a, k;
+	if (f <= 0.) return INT32_MAX;
+	for (i = 0; i < 1<<mi->b; ++i)
+		if (mi->B[i].h) n += kh_size((idxhash_t*)mi->B[i].h);
+	a = (uint32_t*)malloc(n * 4);
+	for (i = n = 0; i < 1<<mi->b; ++i) {
+		idxhash_t *h = (idxhash_t*)mi->B[i].h;
+		if (h == 0) continue;
+		for (k = 0; k < kh_end(h); ++k) {
+			if (!kh_exist(h, k)) continue;
+			a[n++] = kh_key(h, k)&1? 1 : (uint32_t)kh_val(h, k);
+		}
+	}
+	thres = ks_ksmall_uint32_t(n, a, (uint32_t)((1. - f) * n)) + 1;
+	free(a);
+	return thres;
+}
+
+/*********************************
+ * Sort and generate hash tables *
+ *********************************/
+
+static void worker_post(void *g, long i, int tid)
+{
+	int n, n_keys;
+	size_t j, start_a, start_p;
+	idxhash_t *h;
+	mm_idx_t *mi = (mm_idx_t*)g;
+	mm_idx_bucket_t *b = &mi->B[i];
+	if (b->a.n == 0) return;
+
+	// sort by minimizer
+	radix_sort_128x(b->a.a, b->a.a + b->a.n);
+
+	// count and preallocate
+	for (j = 1, n = 1, n_keys = 0, b->n = 0; j <= b->a.n; ++j) {
+		if (j == b->a.n || b->a.a[j].x>>8 != b->a.a[j-1].x>>8) {
+			++n_keys;
+			if (n > 1) b->n += n;
+			n = 1;
+		} else ++n;
+	}
+	h = kh_init(idx);
+	kh_resize(idx, h, n_keys);
+	b->p = (uint64_t*)calloc(b->n, 8);
+
+	// create the hash table
+	for (j = 1, n = 1, start_a = start_p = 0; j <= b->a.n; ++j) {
+		if (j == b->a.n || b->a.a[j].x>>8 != b->a.a[j-1].x>>8) {
+			khint_t itr;
+			int absent;
+			mm128_t *p = &b->a.a[j-1];
+			itr = kh_put(idx, h, p->x>>8>>mi->b<<1, &absent);
+			assert(absent && j == start_a + n);
+			if (n == 1) {
+				kh_key(h, itr) |= 1;
+				kh_val(h, itr) = p->y;
+			} else {
+				int k;
+				for (k = 0; k < n; ++k)
+					b->p[start_p + k] = b->a.a[start_a + k].y;
+				radix_sort_64(&b->p[start_p], &b->p[start_p + n]); // sort by position; needed as in-place radix_sort_128x() is not stable
+				kh_val(h, itr) = (uint64_t)start_p<<32 | n;
+				start_p += n;
+			}
+			start_a = j, n = 1;
+		} else ++n;
+	}
+	b->h = h;
+	assert(b->n == (int32_t)start_p);
+
+	// deallocate and clear b->a
+	kfree(0, b->a.a);
+	b->a.n = b->a.m = 0, b->a.a = 0;
+}
+ 
+static void mm_idx_post(mm_idx_t *mi, int n_threads)
+{
+	kt_for(n_threads, worker_post, mi, 1<<mi->b);
+}
+
+/******************
+ * Generate index *
+ ******************/
+
+#include <string.h>
+#include <zlib.h>
+#include "bseq.h"
+
+typedef struct {
+	int mini_batch_size;
+	uint64_t batch_size, sum_len;
+	mm_bseq_file_t *fp;
+	mm_idx_t *mi;
+} pipeline_t;
+
+typedef struct {
+    int n_seq;
+	mm_bseq1_t *seq;
+	mm128_v a;
+} step_t;
+
+static void mm_idx_add(mm_idx_t *mi, int n, const mm128_t *a)
+{
+	int i, mask = (1<<mi->b) - 1;
+	for (i = 0; i < n; ++i) {
+		mm128_v *p = &mi->B[a[i].x>>8&mask].a;
+		kv_push(mm128_t, 0, *p, a[i]);
+	}
+}
+
+static void *worker_pipeline(void *shared, int step, void *in)
+{
+	int i;
+    pipeline_t *p = (pipeline_t*)shared;
+    if (step == 0) { // step 0: read sequences
+        step_t *s;
+		if (p->sum_len > p->batch_size) return 0;
+        s = (step_t*)calloc(1, sizeof(step_t));
+		s->seq = mm_bseq_read(p->fp, p->mini_batch_size, 0, &s->n_seq); // read a mini-batch
+		if (s->seq) {
+			uint32_t old_m, m;
+			assert((uint64_t)p->mi->n_seq + s->n_seq <= UINT32_MAX); // to prevent integer overflow
+			// make room for p->mi->seq
+			old_m = p->mi->n_seq, m = p->mi->n_seq + s->n_seq;
+			kroundup32(m); kroundup32(old_m);
+			if (old_m != m)
+				p->mi->seq = (mm_idx_seq_t*)krealloc(p->mi->km, p->mi->seq, m * sizeof(mm_idx_seq_t));
+			// make room for p->mi->S
+			if (!(p->mi->flag & MM_I_NO_SEQ)) {
+				uint64_t sum_len, old_max_len, max_len;
+				for (i = 0, sum_len = 0; i < s->n_seq; ++i) sum_len += s->seq[i].l_seq;
+				old_max_len = (p->sum_len + 7) / 8;
+				max_len = (p->sum_len + sum_len + 7) / 8;
+				kroundup64(old_max_len); kroundup64(max_len);
+				if (old_max_len != max_len) {
+					p->mi->S = (uint32_t*)realloc(p->mi->S, max_len * 4);
+					memset(&p->mi->S[old_max_len], 0, 4 * (max_len - old_max_len));
+				}
+			}
+			// populate p->mi->seq
+			for (i = 0; i < s->n_seq; ++i) {
+				mm_idx_seq_t *seq = &p->mi->seq[p->mi->n_seq];
+				uint32_t j;
+				if (!(p->mi->flag & MM_I_NO_NAME)) {
+					seq->name = (char*)kmalloc(p->mi->km, strlen(s->seq[i].name) + 1);
+					strcpy(seq->name, s->seq[i].name);
+				} else seq->name = 0;
+				seq->len = s->seq[i].l_seq;
+				seq->offset = p->sum_len;
+				seq->is_alt = 0;
+				// copy the sequence
+				if (!(p->mi->flag & MM_I_NO_SEQ)) {
+					for (j = 0; j < seq->len; ++j) { // TODO: this is not the fastest way, but let's first see if speed matters here
+						uint64_t o = p->sum_len + j;
+						int c = seq_nt4_table[(uint8_t)s->seq[i].seq[j]];
+						mm_seq4_set(p->mi->S, o, c);
+					}
+				}
+				// update p->sum_len and p->mi->n_seq
+				p->sum_len += seq->len;
+				s->seq[i].rid = p->mi->n_seq++;
+			}
+			return s;
+		} else free(s);
+    } else if (step == 1) { // step 1: compute sketch
+        step_t *s = (step_t*)in;
+		for (i = 0; i < s->n_seq; ++i) {
+			mm_bseq1_t *t = &s->seq[i];
+			if (t->l_seq > 0)
+				mm_sketch(0, t->seq, t->l_seq, p->mi->w, p->mi->k, t->rid, p->mi->flag&MM_I_HPC, &s->a);
+			else if (mm_verbose >= 2)
+				fprintf(stderr, "[WARNING] the length database sequence '%s' is 0\n", t->name);
+			free(t->seq); free(t->name);
+		}
+		free(s->seq); s->seq = 0;
+		return s;
+    } else if (step == 2) { // dispatch sketch to buckets
+        step_t *s = (step_t*)in;
+		mm_idx_add(p->mi, s->a.n, s->a.a);
+		kfree(0, s->a.a); free(s);
+	}
+    return 0;
+}
+
+mm_idx_t *mm_idx_gen(mm_bseq_file_t *fp, int w, int k, int b, int flag, int mini_batch_size, int n_threads, uint64_t batch_size)
+{
+	pipeline_t pl;
+	if (fp == 0 || mm_bseq_eof(fp)) return 0;
+	memset(&pl, 0, sizeof(pipeline_t));
+	pl.mini_batch_size = (uint64_t)mini_batch_size < batch_size? mini_batch_size : batch_size;
+	pl.batch_size = batch_size;
+	pl.fp = fp;
+	pl.mi = mm_idx_init(w, k, b, flag);
+
+	kt_pipeline(n_threads < 3? n_threads : 3, worker_pipeline, &pl, 3);
+	if (mm_verbose >= 3)
+		fprintf(stderr, "[M::%s::%.3f*%.2f] collected minimizers\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0));
+
+	mm_idx_post(pl.mi, n_threads);
+	if (mm_verbose >= 3)
+		fprintf(stderr, "[M::%s::%.3f*%.2f] sorted minimizers\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0));
+
+	return pl.mi;
+}
+
+mm_idx_t *mm_idx_build(const char *fn, int w, int k, int flag, int n_threads) // a simpler interface; deprecated
+{
+	mm_bseq_file_t *fp;
+	mm_idx_t *mi;
+	fp = mm_bseq_open(fn);
+	if (fp == 0) return 0;
+	mi = mm_idx_gen(fp, w, k, 14, flag, 1<<18, n_threads, UINT64_MAX);
+	mm_bseq_close(fp);
+	return mi;
+}
+
+mm_idx_t *mm_idx_str(int w, int k, int is_hpc, int bucket_bits, int n, const char **seq, const char **name)
+{
+	uint64_t sum_len = 0;
+	mm128_v a = {0,0,0};
+	mm_idx_t *mi;
+	khash_t(str) *h;
+	int i, flag = 0;
+
+	if (n <= 0) return 0;
+	for (i = 0; i < n; ++i) // get the total length
+		sum_len += strlen(seq[i]);
+	if (is_hpc) flag |= MM_I_HPC;
+	if (name == 0) flag |= MM_I_NO_NAME;
+	if (bucket_bits < 0) bucket_bits = 14;
+	mi = mm_idx_init(w, k, bucket_bits, flag);
+	mi->n_seq = n;
+	mi->seq = (mm_idx_seq_t*)kcalloc(mi->km, n, sizeof(mm_idx_seq_t)); // ->seq is allocated from km
+	mi->S = (uint32_t*)calloc((sum_len + 7) / 8, 4);
+	mi->h = h = kh_init(str);
+	for (i = 0, sum_len = 0; i < n; ++i) {
+		const char *s = seq[i];
+		mm_idx_seq_t *p = &mi->seq[i];
+		uint32_t j;
+		if (name && name[i]) {
+			int absent;
+			p->name = (char*)kmalloc(mi->km, strlen(name[i]) + 1);
+			strcpy(p->name, name[i]);
+			kh_put(str, h, p->name, &absent);
+			assert(absent);
+		}
+		p->offset = sum_len;
+		p->len = strlen(s);
+		p->is_alt = 0;
+		for (j = 0; j < p->len; ++j) {
+			int c = seq_nt4_table[(uint8_t)s[j]];
+			uint64_t o = sum_len + j;
+			mm_seq4_set(mi->S, o, c);
+		}
+		sum_len += p->len;
+		if (p->len > 0) {
+			a.n = 0;
+			mm_sketch(0, s, p->len, w, k, i, is_hpc, &a);
+			mm_idx_add(mi, a.n, a.a);
+		}
+	}
+	free(a.a);
+	mm_idx_post(mi, 1);
+	return mi;
+}
+
+/*************
+ * index I/O *
+ *************/
+
+void mm_idx_dump(FILE *fp, const mm_idx_t *mi)
+{
+	uint64_t sum_len = 0;
+	uint32_t x[5], i;
+
+	x[0] = mi->w, x[1] = mi->k, x[2] = mi->b, x[3] = mi->n_seq, x[4] = mi->flag;
+	fwrite(MM_IDX_MAGIC, 1, 4, fp);
+	fwrite(x, 4, 5, fp);
+	for (i = 0; i < mi->n_seq; ++i) {
+		if (mi->seq[i].name) {
+			uint8_t l = strlen(mi->seq[i].name);
+			fwrite(&l, 1, 1, fp);
+			fwrite(mi->seq[i].name, 1, l, fp);
+		} else {
+			uint8_t l = 0;
+			fwrite(&l, 1, 1, fp);
+		}
+		fwrite(&mi->seq[i].len, 4, 1, fp);
+		sum_len += mi->seq[i].len;
+	}
+	for (i = 0; i < 1<<mi->b; ++i) {
+		mm_idx_bucket_t *b = &mi->B[i];
+		khint_t k;
+		idxhash_t *h = (idxhash_t*)b->h;
+		uint32_t size = h? h->size : 0;
+		fwrite(&b->n, 4, 1, fp);
+		fwrite(b->p, 8, b->n, fp);
+		fwrite(&size, 4, 1, fp);
+		if (size == 0) continue;
+		for (k = 0; k < kh_end(h); ++k) {
+			uint64_t x[2];
+			if (!kh_exist(h, k)) continue;
+			x[0] = kh_key(h, k), x[1] = kh_val(h, k);
+			fwrite(x, 8, 2, fp);
+		}
+	}
+	if (!(mi->flag & MM_I_NO_SEQ))
+		fwrite(mi->S, 4, (sum_len + 7) / 8, fp);
+	fflush(fp);
+}
+
+mm_idx_t *mm_idx_load(FILE *fp)
+{
+	char magic[4];
+	uint32_t x[5], i;
+	uint64_t sum_len = 0;
+	mm_idx_t *mi;
+
+	if (fread(magic, 1, 4, fp) != 4) return 0;
+	if (strncmp(magic, MM_IDX_MAGIC, 4) != 0) return 0;
+	if (fread(x, 4, 5, fp) != 5) return 0;
+	mi = mm_idx_init(x[0], x[1], x[2], x[4]);
+	mi->n_seq = x[3];
+	mi->seq = (mm_idx_seq_t*)kcalloc(mi->km, mi->n_seq, sizeof(mm_idx_seq_t));
+	for (i = 0; i < mi->n_seq; ++i) {
+		uint8_t l;
+		mm_idx_seq_t *s = &mi->seq[i];
+		fread(&l, 1, 1, fp);
+		if (l) {
+			s->name = (char*)kmalloc(mi->km, l + 1);
+			fread(s->name, 1, l, fp);
+			s->name[l] = 0;
+		}
+		fread(&s->len, 4, 1, fp);
+		s->offset = sum_len;
+		s->is_alt = 0;
+		sum_len += s->len;
+	}
+	for (i = 0; i < 1<<mi->b; ++i) {
+		mm_idx_bucket_t *b = &mi->B[i];
+		uint32_t j, size;
+		khint_t k;
+		idxhash_t *h;
+		fread(&b->n, 4, 1, fp);
+		b->p = (uint64_t*)malloc(b->n * 8);
+		fread(b->p, 8, b->n, fp);
+		fread(&size, 4, 1, fp);
+		if (size == 0) continue;
+		b->h = h = kh_init(idx);
+		kh_resize(idx, h, size);
+		for (j = 0; j < size; ++j) {
+			uint64_t x[2];
+			int absent;
+			fread(x, 8, 2, fp);
+			k = kh_put(idx, h, x[0], &absent);
+			assert(absent);
+			kh_val(h, k) = x[1];
+		}
+	}
+	if (!(mi->flag & MM_I_NO_SEQ)) {
+		mi->S = (uint32_t*)malloc((sum_len + 7) / 8 * 4);
+		fread(mi->S, 4, (sum_len + 7) / 8, fp);
+	}
+	return mi;
+}
+
+int64_t mm_idx_is_idx(const char *fn)
+{
+	int fd, is_idx = 0;
+	int64_t ret, off_end;
+	char magic[4];
+
+	if (strcmp(fn, "-") == 0) return 0; // read from pipe; not an index
+	fd = open(fn, O_RDONLY);
+	if (fd < 0) return -1; // error
+#ifdef WIN32
+	if ((off_end = _lseeki64(fd, 0, SEEK_END)) >= 4) {
+		_lseeki64(fd, 0, SEEK_SET);
+#else
+	if ((off_end = lseek(fd, 0, SEEK_END)) >= 4) {
+		lseek(fd, 0, SEEK_SET);
+#endif // WIN32
+		ret = read(fd, magic, 4);
+		if (ret == 4 && strncmp(magic, MM_IDX_MAGIC, 4) == 0)
+			is_idx = 1;
+	}
+	close(fd);
+	return is_idx? off_end : 0;
+}
+
+mm_idx_reader_t *mm_idx_reader_open(const char *fn, const mm_idxopt_t *opt, const char *fn_out)
+{
+	int64_t is_idx;
+	mm_idx_reader_t *r;
+	is_idx = mm_idx_is_idx(fn);
+	if (is_idx < 0) return 0; // failed to open the index
+	r = (mm_idx_reader_t*)calloc(1, sizeof(mm_idx_reader_t));
+	r->is_idx = is_idx;
+	if (opt) r->opt = *opt;
+	else mm_idxopt_init(&r->opt);
+	if (r->is_idx) {
+		r->fp.idx = fopen(fn, "rb");
+		r->idx_size = is_idx;
+	} else r->fp.seq = mm_bseq_open(fn);
+	if (fn_out) r->fp_out = fopen(fn_out, "wb");
+	return r;
+}
+
+void mm_idx_reader_close(mm_idx_reader_t *r)
+{
+	if (r->is_idx) fclose(r->fp.idx);
+	else mm_bseq_close(r->fp.seq);
+	if (r->fp_out) fclose(r->fp_out);
+	free(r);
+}
+
+mm_idx_t *mm_idx_reader_read(mm_idx_reader_t *r, int n_threads)
+{
+	mm_idx_t *mi;
+	if (r->is_idx) {
+		mi = mm_idx_load(r->fp.idx);
+		if (mi && mm_verbose >= 2 && (mi->k != r->opt.k || mi->w != r->opt.w || (mi->flag&MM_I_HPC) != (r->opt.flag&MM_I_HPC)))
+			fprintf(stderr, "[WARNING]\033[1;31m Indexing parameters (-k, -w or -H) overridden by parameters used in the prebuilt index.\033[0m\n");
+	} else
+		mi = mm_idx_gen(r->fp.seq, r->opt.w, r->opt.k, r->opt.bucket_bits, r->opt.flag, r->opt.mini_batch_size, n_threads, r->opt.batch_size);
+	if (mi) {
+		if (r->fp_out) mm_idx_dump(r->fp_out, mi);
+		mi->index = r->n_parts++;
+	}
+	return mi;
+}
+
+int mm_idx_reader_eof(const mm_idx_reader_t *r) // TODO: in extremely rare cases, mm_bseq_eof() might not work
+{
+	return r->is_idx? (feof(r->fp.idx) || ftell(r->fp.idx) == r->idx_size) : mm_bseq_eof(r->fp.seq);
+}
+
+#include <ctype.h>
+#include <zlib.h>
+#include "ksort.h"
+#include "kseq.h"
+KSTREAM_DECLARE(gzFile, gzread)
+
+int mm_idx_alt_read(mm_idx_t *mi, const char *fn)
+{
+	int n_alt = 0;
+	gzFile fp;
+	kstream_t *ks;
+	kstring_t str = {0,0,0};
+	fp = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+	if (fp == 0) return -1;
+	ks = ks_init(fp);
+	if (mi->h == 0) mm_idx_index_name(mi);
+	while (ks_getuntil(ks, KS_SEP_LINE, &str, 0) >= 0) {
+		char *p;
+		int id;
+		for (p = str.s; *p && !isspace(*p); ++p) { }
+		*p = 0;
+		id = mm_idx_name2id(mi, str.s);
+		if (id >= 0) mi->seq[id].is_alt = 1, ++n_alt;
+	}
+	mi->n_alt = n_alt;
+	if (mm_verbose >= 3)
+		fprintf(stderr, "[M::%s] found %d ALT contigs\n", __func__, n_alt);
+	return n_alt;
+}
+
+#define sort_key_bed(a) ((a).st)
+KRADIX_SORT_INIT(bed, mm_idx_intv1_t, sort_key_bed, 4)
+
+mm_idx_intv_t *mm_idx_read_bed(const mm_idx_t *mi, const char *fn, int read_junc)
+{
+	gzFile fp;
+	kstream_t *ks;
+	kstring_t str = {0,0,0};
+	mm_idx_intv_t *I;
+
+	fp = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+	if (fp == 0) return 0;
+	I = (mm_idx_intv_t*)calloc(mi->n_seq, sizeof(*I));
+	ks = ks_init(fp);
+	while (ks_getuntil(ks, KS_SEP_LINE, &str, 0) >= 0) {
+		mm_idx_intv_t *r;
+		mm_idx_intv1_t t = {-1,-1,-1,-1,0};
+		char *p, *q, *bl, *bs;
+		int32_t i, id = -1, n_blk = 0;
+		for (p = q = str.s, i = 0;; ++p) {
+			if (*p == 0 || *p == '\t') {
+				int32_t c = *p;
+				*p = 0;
+				if (i == 0) { // chr
+					id = mm_idx_name2id(mi, q);
+					if (id < 0) break; // unknown name; TODO: throw a warning
+				} else if (i == 1) { // start
+					t.st = atol(q); // TODO: watch out integer overflow!
+					if (t.st < 0) break;
+				} else if (i == 2) { // end
+					t.en = atol(q);
+					if (t.en < 0) break;
+				} else if (i == 4) { // BED score
+					t.score = atol(q);
+				} else if (i == 5) { // strand
+					t.strand = *q == '+'? 1 : *q == '-'? -1 : 0;
+				} else if (i == 9) {
+					if (!isdigit(*q)) break;
+					n_blk = atol(q);
+				} else if (i == 10) {
+					bl = q;
+				} else if (i == 11) {
+					bs = q;
+					break;
+				}
+				if (c == 0) break;
+				++i, q = p + 1;
+			}
+		}
+		if (id < 0 || t.st < 0 || t.st >= t.en) continue;
+		r = &I[id];
+		if (i >= 11 && read_junc) { // BED12
+			int32_t st, sz, en;
+			st = strtol(bs, &bs, 10); ++bs;
+			sz = strtol(bl, &bl, 10); ++bl;
+			en = t.st + st + sz;
+			for (i = 1; i < n_blk; ++i) {
+				mm_idx_intv1_t s = t;
+				if (r->n == r->m) {
+					r->m = r->m? r->m + (r->m>>1) : 16;
+					r->a = (mm_idx_intv1_t*)realloc(r->a, sizeof(*r->a) * r->m);
+				}
+				st = strtol(bs, &bs, 10); ++bs;
+				sz = strtol(bl, &bl, 10); ++bl;
+				s.st = en, s.en = t.st + st;
+				en = t.st + st + sz;
+				if (s.en > s.st) r->a[r->n++] = s;
+			}
+		} else {
+			if (r->n == r->m) {
+				r->m = r->m? r->m + (r->m>>1) : 16;
+				r->a = (mm_idx_intv1_t*)realloc(r->a, sizeof(*r->a) * r->m);
+			}
+			r->a[r->n++] = t;
+		}
+	}
+	free(str.s);
+	ks_destroy(ks);
+	gzclose(fp);
+	return I;
+}
+
+int mm_idx_bed_read(mm_idx_t *mi, const char *fn, int read_junc)
+{
+	int32_t i;
+	if (mi->h == 0) mm_idx_index_name(mi);
+	mi->I = mm_idx_read_bed(mi, fn, read_junc);
+	if (mi->I == 0) return -1;
+	for (i = 0; i < mi->n_seq; ++i) // TODO: eliminate redundant intervals
+		radix_sort_bed(mi->I[i].a, mi->I[i].a + mi->I[i].n);
+	return 0;
+}
+
+int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, uint8_t *s)
+{
+	int32_t i, left, right;
+	mm_idx_intv_t *r;
+	memset(s, 0, en - st);
+	if (mi->I == 0 || ctg < 0 || ctg >= mi->n_seq) return -1;
+	r = &mi->I[ctg];
+	left = 0, right = r->n;
+	while (right > left) {
+		int32_t mid = left + ((right - left) >> 1);
+		if (r->a[mid].st >= st) right = mid;
+		else left = mid + 1;
+	}
+	for (i = left; i < r->n; ++i) {
+		if (st <= r->a[i].st && en >= r->a[i].en && r->a[i].strand != 0) {
+			if (r->a[i].strand > 0) {
+				s[r->a[i].st - st] |= 1, s[r->a[i].en - 1 - st] |= 2;
+			} else {
+				s[r->a[i].st - st] |= 8, s[r->a[i].en - 1 - st] |= 4;
+			}
+		}
+	}
+	return left;
+}