minimap2 0.2.21 → 0.2.24.0

data/ext/minimap2/setup.py

@@ -0,0 +1,55 @@
+try:
+	from setuptools import setup, Extension
+except ImportError:
+	from distutils.core import setup
+	from distutils.extension import Extension
+
+import sys, platform
+
+sys.path.append('python')
+
+extra_compile_args = ['-DHAVE_KALLOC']
+include_dirs = ["."]
+
+if platform.machine() in ["aarch64", "arm64"]:
+	include_dirs.append("sse2neon/")
+	extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])
+else:
+	extra_compile_args.append('-msse4.1') # WARNING: ancient x86_64 CPUs don't have SSE4
+
+def readme():
+	with open('python/README.rst') as f:
+		return f.read()
+
+setup(
+	name = 'mappy',
+	version = '2.24',
+	url = 'https://github.com/lh3/minimap2',
+	description = 'Minimap2 python binding',
+	long_description = readme(),
+	author = 'Heng Li',
+	author_email = 'lh3@me.com',
+	license = 'MIT',
+	keywords = 'sequence-alignment',
+	scripts = ['python/minimap2.py'],
+	ext_modules = [Extension('mappy',
+		sources = ['python/mappy.pyx', 'align.c', 'bseq.c', 'lchain.c', 'seed.c', 'format.c', 'hit.c', 'index.c', 'pe.c', 'options.c',
+				   'ksw2_extd2_sse.c', 'ksw2_exts2_sse.c', 'ksw2_extz2_sse.c', 'ksw2_ll_sse.c',
+				   'kalloc.c', 'kthread.c', 'map.c', 'misc.c', 'sdust.c', 'sketch.c', 'esterr.c', 'splitidx.c'],
+		depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h',
+				   'ksw2.h', 'kthread.h', 'kvec.h', 'mmpriv.h', 'sdust.h',
+				   'python/cmappy.h', 'python/cmappy.pxd'],
+		extra_compile_args = extra_compile_args,
+		include_dirs = include_dirs,
+		libraries = ['z', 'm', 'pthread'])],
+	classifiers = [
+		'Development Status :: 5 - Production/Stable',
+		'License :: OSI Approved :: MIT License',
+		'Operating System :: POSIX',
+		'Programming Language :: C',
+		'Programming Language :: Cython',
+		'Programming Language :: Python :: 2.7',
+		'Programming Language :: Python :: 3',
+		'Intended Audience :: Science/Research',
+		'Topic :: Scientific/Engineering :: Bio-Informatics'],
+	setup_requires=["cython"])

data/ext/minimap2/sketch.c

@@ -0,0 +1,143 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <assert.h>
+#include <string.h>
+#define __STDC_LIMIT_MACROS
+#include "kvec.h"
+#include "mmpriv.h"
+
+unsigned char seq_nt4_table[256] = {
+	0, 1, 2, 3,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
+	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4,
+	4, 4, 4, 4,  3, 3, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
+	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4,
+	4, 4, 4, 4,  3, 3, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
+	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4
+};
+
+static inline uint64_t hash64(uint64_t key, uint64_t mask)
+{
+	key = (~key + (key << 21)) & mask; // key = (key << 21) - key - 1;
+	key = key ^ key >> 24;
+	key = ((key + (key << 3)) + (key << 8)) & mask; // key * 265
+	key = key ^ key >> 14;
+	key = ((key + (key << 2)) + (key << 4)) & mask; // key * 21
+	key = key ^ key >> 28;
+	key = (key + (key << 31)) & mask;
+	return key;
+}
+
+typedef struct { // a simplified version of kdq
+	int front, count;
+	int a[32];
+} tiny_queue_t;
+
+static inline void tq_push(tiny_queue_t *q, int x)
+{
+	q->a[((q->count++) + q->front) & 0x1f] = x;
+}
+
+static inline int tq_shift(tiny_queue_t *q)
+{
+	int x;
+	if (q->count == 0) return -1;
+	x = q->a[q->front++];
+	q->front &= 0x1f;
+	--q->count;
+	return x;
+}
+
+/**
+ * Find symmetric (w,k)-minimizers on a DNA sequence
+ *
+ * @param km     thread-local memory pool; using NULL falls back to malloc()
+ * @param str    DNA sequence
+ * @param len    length of $str
+ * @param w      find a minimizer for every $w consecutive k-mers
+ * @param k      k-mer size
+ * @param rid    reference ID; will be copied to the output $p array
+ * @param is_hpc homopolymer-compressed or not
+ * @param p      minimizers
+ *               p->a[i].x = kMer<<8 | kmerSpan
+ *               p->a[i].y = rid<<32 | lastPos<<1 | strand
+ *               where lastPos is the position of the last base of the i-th minimizer,
+ *               and strand indicates whether the minimizer comes from the top or the bottom strand.
+ *               Callers may want to set "p->n = 0"; otherwise results are appended to p
+ */
+void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, int is_hpc, mm128_v *p)
+{
+	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[256], min = { UINT64_MAX, UINT64_MAX };
+	tiny_queue_t tq;
+
+	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);
+
+	for (i = l = buf_pos = min_pos = 0; i < len; ++i) {
+		int c = seq_nt4_table[(uint8_t)str[i]];
+		mm128_t info = { UINT64_MAX, UINT64_MAX };
+		if (c < 4) { // not an ambiguous base
+			int z;
+			if (is_hpc) {
+				int skip_len = 1;
+				if (i + 1 < len && seq_nt4_table[(uint8_t)str[i + 1]] == c) {
+					for (skip_len = 2; i + skip_len < len; ++skip_len)
+						if (seq_nt4_table[(uint8_t)str[i + skip_len]] != c)
+							break;
+					i += skip_len - 1; // put $i at the end of the current homopolymer run
+				}
+				tq_push(&tq, skip_len);
+				kmer_span += skip_len;
+				if (tq.count > k) kmer_span -= tq_shift(&tq);
+			} else kmer_span = l + 1 < k? l + 1 : k;
+			kmer[0] = (kmer[0] << 2 | c) & mask;           // forward k-mer
+			kmer[1] = (kmer[1] >> 2) | (3ULL^c) << shift1; // reverse k-mer
+			if (kmer[0] == kmer[1]) continue; // skip "symmetric k-mers" as we don't know it strand
+			z = kmer[0] < kmer[1]? 0 : 1; // strand
+			++l;
+			if (l >= k && kmer_span < 256) {
+				info.x = hash64(kmer[z], mask) << 8 | kmer_span;
+				info.y = (uint64_t)rid<<32 | (uint32_t)i<<1 | z;
+			}
+		} else l = 0, tq.count = tq.front = 0, kmer_span = 0;
+		buf[buf_pos] = info; // need to do this here as appropriate buf_pos and buf[buf_pos] are needed below
+		if (l == w + k - 1 && min.x != UINT64_MAX) { // special case for the first window - because identical k-mers are not stored yet
+			for (j = buf_pos + 1; j < w; ++j)
+				if (min.x == buf[j].x && buf[j].y != min.y) kv_push(mm128_t, km, *p, buf[j]);
+			for (j = 0; j < buf_pos; ++j)
+				if (min.x == buf[j].x && buf[j].y != min.y) kv_push(mm128_t, km, *p, buf[j]);
+		}
+		if (info.x <= min.x) { // a new minimum; then write the old min
+			if (l >= w + k && min.x != UINT64_MAX) kv_push(mm128_t, km, *p, min);
+			min = info, min_pos = buf_pos;
+		} else if (buf_pos == min_pos) { // old min has moved outside the window
+			if (l >= w + k - 1 && min.x != UINT64_MAX) kv_push(mm128_t, km, *p, min);
+			for (j = buf_pos + 1, min.x = UINT64_MAX; j < w; ++j) // the two loops are necessary when there are identical k-mers
+				if (min.x >= buf[j].x) min = buf[j], min_pos = j; // >= is important s.t. min is always the closest k-mer
+			for (j = 0; j <= buf_pos; ++j)
+				if (min.x >= buf[j].x) min = buf[j], min_pos = j;
+			if (l >= w + k - 1 && min.x != UINT64_MAX) { // write identical k-mers
+				for (j = buf_pos + 1; j < w; ++j) // these two loops make sure the output is sorted
+					if (min.x == buf[j].x && min.y != buf[j].y) kv_push(mm128_t, km, *p, buf[j]);
+				for (j = 0; j <= buf_pos; ++j)
+					if (min.x == buf[j].x && min.y != buf[j].y) kv_push(mm128_t, km, *p, buf[j]);
+			}
+		}
+		if (++buf_pos == w) buf_pos = 0;
+	}
+	if (min.x != UINT64_MAX)
+		kv_push(mm128_t, km, *p, min);
+}

data/ext/minimap2/splitidx.c

@@ -0,0 +1,84 @@
+#include <string.h>
+#include <assert.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <errno.h>
+#include "mmpriv.h"
+
+FILE *mm_split_init(const char *prefix, const mm_idx_t *mi)
+{
+	char *fn;
+	FILE *fp;
+	uint32_t i, k = mi->k;
+	fn = (char*)calloc(strlen(prefix) + 10, 1);
+	sprintf(fn, "%s.%.4d.tmp", prefix, mi->index);
+	if ((fp = fopen(fn, "wb")) == NULL) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m failed to write to temporary file '%s'\033[0m: %s\n", fn, strerror(errno));
+		exit(1);
+	}
+	mm_err_fwrite(&k, 4, 1, fp);
+	mm_err_fwrite(&mi->n_seq, 4, 1, fp);
+	for (i = 0; i < mi->n_seq; ++i) {
+		uint32_t l;
+		l = strlen(mi->seq[i].name);
+		mm_err_fwrite(&l, 1, 4, fp);
+		mm_err_fwrite(mi->seq[i].name, 1, l, fp);
+		mm_err_fwrite(&mi->seq[i].len, 4, 1, fp);
+	}
+	free(fn);
+	return fp;
+}
+
+mm_idx_t *mm_split_merge_prep(const char *prefix, int n_splits, FILE **fp, uint32_t *n_seq_part)
+{
+	mm_idx_t *mi = 0;
+	char *fn;
+	int i, j;
+
+	if (n_splits < 1) return 0;
+	fn = CALLOC(char, strlen(prefix) + 10);
+	for (i = 0; i < n_splits; ++i) {
+		sprintf(fn, "%s.%.4d.tmp", prefix, i);
+		if ((fp[i] = fopen(fn, "rb")) == 0) {
+			if (mm_verbose >= 1)
+				fprintf(stderr, "ERROR: failed to open temporary file '%s': %s\n", fn, strerror(errno));
+			for (j = 0; j < i; ++j)
+				fclose(fp[j]);
+			free(fn);
+			return 0;
+		}
+	}
+	free(fn);
+
+	mi = CALLOC(mm_idx_t, 1);
+	for (i = 0; i < n_splits; ++i) {
+		mm_err_fread(&mi->k, 4, 1, fp[i]); // TODO: check if k is all the same
+		mm_err_fread(&n_seq_part[i], 4, 1, fp[i]);
+		mi->n_seq += n_seq_part[i];
+	}
+	mi->seq = CALLOC(mm_idx_seq_t, mi->n_seq);
+	for (i = j = 0; i < n_splits; ++i) {
+		uint32_t k;
+		for (k = 0; k < n_seq_part[i]; ++k, ++j) {
+			uint32_t l;
+			mm_err_fread(&l, 1, 4, fp[i]);
+			mi->seq[j].name = (char*)calloc(l + 1, 1);
+			mm_err_fread(mi->seq[j].name, 1, l, fp[i]);
+			mm_err_fread(&mi->seq[j].len, 4, 1, fp[i]);
+		}
+	}
+	return mi;
+}
+
+void mm_split_rm_tmp(const char *prefix, int n_splits)
+{
+	int i;
+	char *fn;
+	fn = CALLOC(char, strlen(prefix) + 10);
+	for (i = 0; i < n_splits; ++i) {
+		sprintf(fn, "%s.%.4d.tmp", prefix, i);
+		remove(fn);
+	}
+	free(fn);
+}