--- /dev/null
+#include "pysam.h"
+
+#include <ctype.h>
+#include <assert.h>
+#include <sys/stat.h>
+#include "khash.h"
+#include "ksort.h"
+#include "kstring.h"
+#include "bam_endian.h"
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+#include "tabix.h"
+
+#define TAD_MIN_CHUNK_GAP 32768
+// 1<<14 is the size of minimum bin.
+#define TAD_LIDX_SHIFT 14
+
+typedef struct {
+ uint64_t u, v;
+} pair64_t;
+
+#define pair64_lt(a,b) ((a).u < (b).u)
+KSORT_INIT(offt, pair64_t, pair64_lt)
+
+typedef struct {
+ uint32_t m, n;
+ pair64_t *list;
+} ti_binlist_t;
+
+typedef struct {
+ int32_t n, m;
+ uint64_t *offset;
+} ti_lidx_t;
+
+KHASH_MAP_INIT_INT(i, ti_binlist_t)
+KHASH_MAP_INIT_STR(s, int)
+
+struct __ti_index_t {
+ ti_conf_t conf;
+ int32_t n, max;
+ khash_t(s) *tname;
+ khash_t(i) **index;
+ ti_lidx_t *index2;
+};
+
+struct __ti_iter_t {
+ int from_first; // read from the first record; no random access
+ int tid, beg, end, n_off, i, finished;
+ uint64_t curr_off;
+ kstring_t str;
+ const ti_index_t *idx;
+ pair64_t *off;
+};
+
+typedef struct {
+ int tid, beg, end, bin;
+} ti_intv_t;
+
+ti_conf_t ti_conf_gff = { 0, 1, 4, 5, '#', 0 };
+ti_conf_t ti_conf_bed = { TI_FLAG_UCSC, 1, 2, 3, '#', 0 };
+ti_conf_t ti_conf_psltbl = { TI_FLAG_UCSC, 15, 17, 18, '#', 0 };
+ti_conf_t ti_conf_sam = { TI_PRESET_SAM, 3, 4, 0, '@', 0 };
+ti_conf_t ti_conf_vcf = { TI_PRESET_VCF, 1, 2, 0, '#', 0 };
+
+/***************
+ * read a line *
+ ***************/
+
+/*
+int ti_readline(BGZF *fp, kstring_t *str)
+{
+ int c, l = 0;
+ str->l = 0;
+ while ((c = bgzf_getc(fp)) >= 0 && c != '\n') {
+ ++l;
+ if (c != '\r') kputc(c, str);
+ }
+ if (c < 0 && l == 0) return -1; // end of file
+ return str->l;
+}
+*/
+
+/* Below is a faster implementation largely equivalent to the one
+ * commented out above. */
+int ti_readline(BGZF *fp, kstring_t *str)
+{
+ int l, state = 0;
+ unsigned char *buf = (unsigned char*)fp->uncompressed_block;
+ str->l = 0;
+ do {
+ if (fp->block_offset >= fp->block_length) {
+ if (bgzf_read_block(fp) != 0) { state = -2; break; }
+ if (fp->block_length == 0) { state = -1; break; }
+ }
+ for (l = fp->block_offset; l < fp->block_length && buf[l] != '\n'; ++l);
+ if (l < fp->block_length) state = 1;
+ l -= fp->block_offset;
+ if (str->l + l + 1 >= str->m) {
+ str->m = str->l + l + 2;
+ kroundup32(str->m);
+ str->s = (char*)realloc(str->s, str->m);
+ }
+ memcpy(str->s + str->l, buf + fp->block_offset, l);
+ str->l += l;
+ fp->block_offset += l + 1;
+ if (fp->block_offset >= fp->block_length) {
+#ifdef _USE_KNETFILE
+ fp->block_address = knet_tell(fp->x.fpr);
+#else
+ fp->block_address = ftello(fp->file);
+#endif
+ fp->block_offset = 0;
+ fp->block_length = 0;
+ }
+ } while (state == 0);
+ if (str->l == 0 && state < 0) return state;
+ str->s[str->l] = 0;
+ return str->l;
+}
+
+/*************************************
+ * get the interval from a data line *
+ *************************************/
+
+static inline int ti_reg2bin(uint32_t beg, uint32_t end)
+{
+ --end;
+ if (beg>>14 == end>>14) return 4681 + (beg>>14);
+ if (beg>>17 == end>>17) return 585 + (beg>>17);
+ if (beg>>20 == end>>20) return 73 + (beg>>20);
+ if (beg>>23 == end>>23) return 9 + (beg>>23);
+ if (beg>>26 == end>>26) return 1 + (beg>>26);
+ return 0;
+}
+
+static int get_tid(ti_index_t *idx, const char *ss)
+{
+ khint_t k;
+ int tid;
+ k = kh_get(s, idx->tname, ss);
+ if (k == kh_end(idx->tname)) { // a new target sequence
+ int ret, size;
+ // update idx->n, ->max, ->index and ->index2
+ if (idx->n == idx->max) {
+ idx->max = idx->max? idx->max<<1 : 8;
+ idx->index = realloc(idx->index, idx->max * sizeof(void*));
+ idx->index2 = realloc(idx->index2, idx->max * sizeof(ti_lidx_t));
+ }
+ memset(&idx->index2[idx->n], 0, sizeof(ti_lidx_t));
+ idx->index[idx->n++] = kh_init(i);
+ // update ->tname
+ tid = size = kh_size(idx->tname);
+ k = kh_put(s, idx->tname, strdup(ss), &ret);
+ kh_value(idx->tname, k) = size;
+ assert(idx->n == kh_size(idx->tname));
+ } else tid = kh_value(idx->tname, k);
+ return tid;
+}
+
+int ti_get_intv(const ti_conf_t *conf, int len, char *line, ti_interval_t *intv)
+{
+ int i, b = 0, id = 1, ncols = 0;
+ char *s;
+ intv->ss = intv->se = 0; intv->beg = intv->end = -1;
+ for (i = 0; i <= len; ++i) {
+ if (line[i] == '\t' || line[i] == 0) {
+ ++ncols;
+ if (id == conf->sc) {
+ intv->ss = line + b; intv->se = line + i;
+ } else if (id == conf->bc) {
+ // here ->beg is 0-based.
+ intv->beg = intv->end = strtol(line + b, &s, 0);
+ if (!(conf->preset&TI_FLAG_UCSC)) --intv->beg;
+ else ++intv->end;
+ if (intv->beg < 0) intv->beg = 0;
+ if (intv->end < 1) intv->end = 1;
+ } else {
+ if ((conf->preset&0xffff) == TI_PRESET_GENERIC) {
+ if (id == conf->ec) intv->end = strtol(line + b, &s, 0);
+ } else if ((conf->preset&0xffff) == TI_PRESET_SAM) {
+ if (id == 6) { // CIGAR
+ int l = 0, op;
+ char *t;
+ for (s = line + b; s < line + i;) {
+ long x = strtol(s, &t, 10);
+ op = toupper(*t);
+ if (op == 'M' || op == 'D' || op == 'N') l += x;
+ s = t + 1;
+ }
+ if (l == 0) l = 1;
+ intv->end = intv->beg + l;
+ }
+ } else if ((conf->preset&0xffff) == TI_PRESET_VCF) {
+ // FIXME: the following is NOT tested and is likely to be buggy
+ if (id == 4) {
+ if (b < i) intv->end = intv->beg + (i - b);
+ } else if (id == 8) { // look for "END="
+ int c = line[i];
+ line[i] = 0;
+ s = strstr(line + b, "END=");
+ if (s == line + b) s += 4;
+ else if (s) {
+ s = strstr(line + b, ";END=");
+ if (s) s += 5;
+ }
+ if (s) intv->end = strtol(s, &s, 0);
+ line[i] = c;
+ }
+ }
+ }
+ b = i + 1;
+ ++id;
+ }
+ }
+/*
+ if (ncols < conf->sc || ncols < conf->bc || ncols < conf->ec) {
+ if (ncols == 1) fprintf(pysamerr,"[get_intv] Is the file tab-delimited? The line has %d field only: %s\n", ncols, line);
+ else fprintf(pysamerr,"[get_intv] The line has %d field(s) only: %s\n", ncols, line);
+ exit(1);
+ }
+*/
+ if (intv->ss == 0 || intv->se == 0 || intv->beg < 0 || intv->end < 0) return -1;
+ return 0;
+}
+
+static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
+{
+ ti_interval_t x;
+ intv->tid = intv->beg = intv->end = intv->bin = -1;
+ if (ti_get_intv(&idx->conf, str->l, str->s, &x) == 0) {
+ int c = *x.se;
+ *x.se = '\0'; intv->tid = get_tid(idx, x.ss); *x.se = c;
+ intv->beg = x.beg; intv->end = x.end;
+ intv->bin = ti_reg2bin(intv->beg, intv->end);
+ return (intv->tid >= 0 && intv->beg >= 0 && intv->end >= 0)? 0 : -1;
+ } else {
+ fprintf(pysamerr, "[%s] the following line cannot be parsed and skipped: %s\n", __func__, str->s);
+ return -1;
+ }
+}
+
+/************
+ * indexing *
+ ************/
+
+// requirement: len <= LEN_MASK
+static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t end)
+{
+ khint_t k;
+ ti_binlist_t *l;
+ int ret;
+ k = kh_put(i, h, bin, &ret);
+ l = &kh_value(h, k);
+ if (ret) { // not present
+ l->m = 1; l->n = 0;
+ l->list = (pair64_t*)calloc(l->m, 16);
+ }
+ if (l->n == l->m) {
+ l->m <<= 1;
+ l->list = (pair64_t*)realloc(l->list, l->m * 16);
+ }
+ l->list[l->n].u = beg; l->list[l->n++].v = end;
+}
+
+static inline uint64_t insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_t offset)
+{
+ int i, beg, end;
+ beg = _beg >> TAD_LIDX_SHIFT;
+ end = (_end - 1) >> TAD_LIDX_SHIFT;
+ if (index2->m < end + 1) {
+ int old_m = index2->m;
+ index2->m = end + 1;
+ kroundup32(index2->m);
+ index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
+ memset(index2->offset + old_m, 0, 8 * (index2->m - old_m));
+ }
+ if (beg == end) {
+ if (index2->offset[beg] == 0) index2->offset[beg] = offset;
+ } else {
+ for (i = beg; i <= end; ++i)
+ if (index2->offset[i] == 0) index2->offset[i] = offset;
+ }
+ if (index2->n < end + 1) index2->n = end + 1;
+ return (uint64_t)beg<<32 | end;
+}
+
+static void merge_chunks(ti_index_t *idx)
+{
+ khash_t(i) *index;
+ int i, l, m;
+ khint_t k;
+ for (i = 0; i < idx->n; ++i) {
+ index = idx->index[i];
+ for (k = kh_begin(index); k != kh_end(index); ++k) {
+ ti_binlist_t *p;
+ if (!kh_exist(index, k)) continue;
+ p = &kh_value(index, k);
+ m = 0;
+ for (l = 1; l < p->n; ++l) {
+ if (p->list[m].v>>16 == p->list[l].u>>16) p->list[m].v = p->list[l].v;
+ else p->list[++m] = p->list[l];
+ } // ~for(l)
+ p->n = m + 1;
+ } // ~for(k)
+ } // ~for(i)
+}
+
+static void fill_missing(ti_index_t *idx)
+{
+ int i, j;
+ for (i = 0; i < idx->n; ++i) {
+ ti_lidx_t *idx2 = &idx->index2[i];
+ for (j = 1; j < idx2->n; ++j)
+ if (idx2->offset[j] == 0)
+ idx2->offset[j] = idx2->offset[j-1];
+ }
+}
+
+ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf)
+{
+ int ret;
+ ti_index_t *idx;
+ uint32_t last_bin, save_bin;
+ int32_t last_coor, last_tid, save_tid;
+ uint64_t save_off, last_off, lineno = 0, offset0 = (uint64_t)-1, tmp;
+ kstring_t *str;
+
+ str = calloc(1, sizeof(kstring_t));
+
+ idx = (ti_index_t*)calloc(1, sizeof(ti_index_t));
+ idx->conf = *conf;
+ idx->n = idx->max = 0;
+ idx->tname = kh_init(s);
+ idx->index = 0;
+ idx->index2 = 0;
+
+ save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
+ save_off = last_off = bgzf_tell(fp); last_coor = 0xffffffffu;
+ while ((ret = ti_readline(fp, str)) >= 0) {
+ ti_intv_t intv;
+ ++lineno;
+ if (lineno <= idx->conf.line_skip || str->s[0] == idx->conf.meta_char) {
+ last_off = bgzf_tell(fp);
+ continue;
+ }
+ get_intv(idx, str, &intv);
+ if ( intv.beg<0 || intv.end<0 )
+ {
+ fprintf(pysamerr,"[ti_index_core] the indexes overlap or are out of bounds\n");
+ exit(1);
+ }
+ if (last_tid != intv.tid) { // change of chromosomes
+ if (last_tid>intv.tid )
+ {
+ fprintf(pysamerr,"[ti_index_core] the chromosome blocks not continuous at line %llu, is the file sorted? [pos %d]\n",(unsigned long long)lineno,intv.beg+1);
+ exit(1);
+ }
+ last_tid = intv.tid;
+ last_bin = 0xffffffffu;
+ } else if (last_coor > intv.beg) {
+ fprintf(pysamerr, "[ti_index_core] the file out of order at line %llu\n", (unsigned long long)lineno);
+ exit(1);
+ }
+ tmp = insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off);
+ if (last_off == 0) offset0 = tmp;
+ if (intv.bin != last_bin) { // then possibly write the binning index
+ if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
+ insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
+ save_off = last_off;
+ save_bin = last_bin = intv.bin;
+ save_tid = intv.tid;
+ if (save_tid < 0) break;
+ }
+ if (bgzf_tell(fp) <= last_off) {
+ fprintf(pysamerr, "[ti_index_core] bug in BGZF: %llx < %llx\n",
+ (unsigned long long)bgzf_tell(fp), (unsigned long long)last_off);
+ exit(1);
+ }
+ last_off = bgzf_tell(fp);
+ last_coor = intv.beg;
+ }
+ if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bgzf_tell(fp));
+ merge_chunks(idx);
+ fill_missing(idx);
+ if (offset0 != (uint64_t)-1 && idx->n && idx->index2[0].offset) {
+ int i, beg = offset0>>32, end = offset0&0xffffffffu;
+ for (i = beg; i <= end; ++i) idx->index2[0].offset[i] = 0;
+ }
+
+ free(str->s); free(str);
+ return idx;
+}
+
+void ti_index_destroy(ti_index_t *idx)
+{
+ khint_t k;
+ int i;
+ if (idx == 0) return;
+ // destroy the name hash table
+ for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k) {
+ if (kh_exist(idx->tname, k))
+ free((char*)kh_key(idx->tname, k));
+ }
+ kh_destroy(s, idx->tname);
+ // destroy the binning index
+ for (i = 0; i < idx->n; ++i) {
+ khash_t(i) *index = idx->index[i];
+ ti_lidx_t *index2 = idx->index2 + i;
+ for (k = kh_begin(index); k != kh_end(index); ++k) {
+ if (kh_exist(index, k))
+ free(kh_value(index, k).list);
+ }
+ kh_destroy(i, index);
+ free(index2->offset);
+ }
+ free(idx->index);
+ // destroy the linear index
+ free(idx->index2);
+ free(idx);
+}
+
+/******************
+ * index file I/O *
+ ******************/
+
+void ti_index_save(const ti_index_t *idx, BGZF *fp)
+{
+ int32_t i, size, ti_is_be;
+ khint_t k;
+ ti_is_be = bam_is_big_endian();
+ bgzf_write(fp, "TBI\1", 4);
+ if (ti_is_be) {
+ uint32_t x = idx->n;
+ bgzf_write(fp, bam_swap_endian_4p(&x), 4);
+ } else bgzf_write(fp, &idx->n, 4);
+ assert(sizeof(ti_conf_t) == 24);
+ if (ti_is_be) { // write ti_conf_t;
+ uint32_t x[6];
+ memcpy(x, &idx->conf, 24);
+ for (i = 0; i < 6; ++i) bgzf_write(fp, bam_swap_endian_4p(&x[i]), 4);
+ } else bgzf_write(fp, &idx->conf, sizeof(ti_conf_t));
+ { // write target names
+ char **name;
+ int32_t l = 0;
+ name = calloc(kh_size(idx->tname), sizeof(void*));
+ for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k)
+ if (kh_exist(idx->tname, k))
+ name[kh_value(idx->tname, k)] = (char*)kh_key(idx->tname, k);
+ for (i = 0; i < kh_size(idx->tname); ++i)
+ l += strlen(name[i]) + 1;
+ if (ti_is_be) bgzf_write(fp, bam_swap_endian_4p(&l), 4);
+ else bgzf_write(fp, &l, 4);
+ for (i = 0; i < kh_size(idx->tname); ++i)
+ bgzf_write(fp, name[i], strlen(name[i]) + 1);
+ free(name);
+ }
+ for (i = 0; i < idx->n; ++i) {
+ khash_t(i) *index = idx->index[i];
+ ti_lidx_t *index2 = idx->index2 + i;
+ // write binning index
+ size = kh_size(index);
+ if (ti_is_be) { // big endian
+ uint32_t x = size;
+ bgzf_write(fp, bam_swap_endian_4p(&x), 4);
+ } else bgzf_write(fp, &size, 4);
+ for (k = kh_begin(index); k != kh_end(index); ++k) {
+ if (kh_exist(index, k)) {
+ ti_binlist_t *p = &kh_value(index, k);
+ if (ti_is_be) { // big endian
+ uint32_t x;
+ x = kh_key(index, k); bgzf_write(fp, bam_swap_endian_4p(&x), 4);
+ x = p->n; bgzf_write(fp, bam_swap_endian_4p(&x), 4);
+ for (x = 0; (int)x < p->n; ++x) {
+ bam_swap_endian_8p(&p->list[x].u);
+ bam_swap_endian_8p(&p->list[x].v);
+ }
+ bgzf_write(fp, p->list, 16 * p->n);
+ for (x = 0; (int)x < p->n; ++x) {
+ bam_swap_endian_8p(&p->list[x].u);
+ bam_swap_endian_8p(&p->list[x].v);
+ }
+ } else {
+ bgzf_write(fp, &kh_key(index, k), 4);
+ bgzf_write(fp, &p->n, 4);
+ bgzf_write(fp, p->list, 16 * p->n);
+ }
+ }
+ }
+ // write linear index (index2)
+ if (ti_is_be) {
+ int x = index2->n;
+ bgzf_write(fp, bam_swap_endian_4p(&x), 4);
+ } else bgzf_write(fp, &index2->n, 4);
+ if (ti_is_be) { // big endian
+ int x;
+ for (x = 0; (int)x < index2->n; ++x)
+ bam_swap_endian_8p(&index2->offset[x]);
+ bgzf_write(fp, index2->offset, 8 * index2->n);
+ for (x = 0; (int)x < index2->n; ++x)
+ bam_swap_endian_8p(&index2->offset[x]);
+ } else bgzf_write(fp, index2->offset, 8 * index2->n);
+ }
+}
+
+static ti_index_t *ti_index_load_core(BGZF *fp)
+{
+ int i, ti_is_be;
+ char magic[4];
+ ti_index_t *idx;
+ ti_is_be = bam_is_big_endian();
+ if (fp == 0) {
+ fprintf(pysamerr, "[ti_index_load_core] fail to load index.\n");
+ return 0;
+ }
+ bgzf_read(fp, magic, 4);
+ if (strncmp(magic, "TBI\1", 4)) {
+ fprintf(pysamerr, "[ti_index_load] wrong magic number.\n");
+ return 0;
+ }
+ idx = (ti_index_t*)calloc(1, sizeof(ti_index_t));
+ bgzf_read(fp, &idx->n, 4);
+ if (ti_is_be) bam_swap_endian_4p(&idx->n);
+ idx->tname = kh_init(s);
+ idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
+ idx->index2 = (ti_lidx_t*)calloc(idx->n, sizeof(ti_lidx_t));
+ // read idx->conf
+ bgzf_read(fp, &idx->conf, sizeof(ti_conf_t));
+ if (ti_is_be) {
+ bam_swap_endian_4p(&idx->conf.preset);
+ bam_swap_endian_4p(&idx->conf.sc);
+ bam_swap_endian_4p(&idx->conf.bc);
+ bam_swap_endian_4p(&idx->conf.ec);
+ bam_swap_endian_4p(&idx->conf.meta_char);
+ bam_swap_endian_4p(&idx->conf.line_skip);
+ }
+ { // read target names
+ int j, ret;
+ kstring_t *str;
+ int32_t l;
+ uint8_t *buf;
+ bgzf_read(fp, &l, 4);
+ if (ti_is_be) bam_swap_endian_4p(&l);
+ buf = calloc(l, 1);
+ bgzf_read(fp, buf, l);
+ str = calloc(1, sizeof(kstring_t));
+ for (i = j = 0; i < l; ++i) {
+ if (buf[i] == 0) {
+ khint_t k = kh_put(s, idx->tname, strdup(str->s), &ret);
+ kh_value(idx->tname, k) = j++;
+ str->l = 0;
+ } else kputc(buf[i], str);
+ }
+ free(str->s); free(str); free(buf);
+ }
+ for (i = 0; i < idx->n; ++i) {
+ khash_t(i) *index;
+ ti_lidx_t *index2 = idx->index2 + i;
+ uint32_t key, size;
+ khint_t k;
+ int j, ret;
+ ti_binlist_t *p;
+ index = idx->index[i] = kh_init(i);
+ // load binning index
+ bgzf_read(fp, &size, 4);
+ if (ti_is_be) bam_swap_endian_4p(&size);
+ for (j = 0; j < (int)size; ++j) {
+ bgzf_read(fp, &key, 4);
+ if (ti_is_be) bam_swap_endian_4p(&key);
+ k = kh_put(i, index, key, &ret);
+ p = &kh_value(index, k);
+ bgzf_read(fp, &p->n, 4);
+ if (ti_is_be) bam_swap_endian_4p(&p->n);
+ p->m = p->n;
+ p->list = (pair64_t*)malloc(p->m * 16);
+ bgzf_read(fp, p->list, 16 * p->n);
+ if (ti_is_be) {
+ int x;
+ for (x = 0; x < p->n; ++x) {
+ bam_swap_endian_8p(&p->list[x].u);
+ bam_swap_endian_8p(&p->list[x].v);
+ }
+ }
+ }
+ // load linear index
+ bgzf_read(fp, &index2->n, 4);
+ if (ti_is_be) bam_swap_endian_4p(&index2->n);
+ index2->m = index2->n;
+ index2->offset = (uint64_t*)calloc(index2->m, 8);
+ bgzf_read(fp, index2->offset, index2->n * 8);
+ if (ti_is_be)
+ for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
+ }
+ return idx;
+}
+
+ti_index_t *ti_index_load_local(const char *fnidx)
+{
+ BGZF *fp;
+ fp = bgzf_open(fnidx, "r");
+ if (fp) {
+ ti_index_t *idx = ti_index_load_core(fp);
+ bgzf_close(fp);
+ return idx;
+ } else return 0;
+}
+
+#ifdef _USE_KNETFILE
+static void download_from_remote(const char *url)
+{
+ const int buf_size = 1 * 1024 * 1024;
+ char *fn;
+ FILE *fp;
+ uint8_t *buf;
+ knetFile *fp_remote;
+ int l;
+ if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return;
+ l = strlen(url);
+ for (fn = (char*)url + l - 1; fn >= url; --fn)
+ if (*fn == '/') break;
+ ++fn; // fn now points to the file name
+ fp_remote = knet_open(url, "r");
+ if (fp_remote == 0) {
+ fprintf(pysamerr, "[download_from_remote] fail to open remote file.\n");
+ return;
+ }
+ if ((fp = fopen(fn, "w")) == 0) {
+ fprintf(pysamerr, "[download_from_remote] fail to create file in the working directory.\n");
+ knet_close(fp_remote);
+ return;
+ }
+ buf = (uint8_t*)calloc(buf_size, 1);
+ while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
+ fwrite(buf, 1, l, fp);
+ free(buf);
+ fclose(fp);
+ knet_close(fp_remote);
+}
+#else
+static void download_from_remote(const char *url)
+{
+ return;
+}
+#endif
+
+static char *get_local_version(const char *fn)
+{
+ struct stat sbuf;
+ char *fnidx = (char*)calloc(strlen(fn) + 5, 1);
+ strcat(strcpy(fnidx, fn), ".tbi");
+ if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) {
+ char *p, *url;
+ int l = strlen(fnidx);
+ for (p = fnidx + l - 1; p >= fnidx; --p)
+ if (*p == '/') break;
+ url = fnidx; fnidx = strdup(p + 1);
+ if (stat(fnidx, &sbuf) == 0) {
+ free(url);
+ return fnidx;
+ }
+ fprintf(pysamerr, "[%s] downloading the index file...\n", __func__);
+ download_from_remote(url);
+ free(url);
+ }
+ if (stat(fnidx, &sbuf) == 0) return fnidx;
+ free(fnidx); return 0;
+}
+
+const char **ti_seqname(const ti_index_t *idx, int *n)
+{
+ const char **names;
+ khint_t k;
+ *n = idx->n;
+ names = calloc(idx->n, sizeof(void*));
+ for (k = kh_begin(idx->tname); k < kh_end(idx->tname); ++k)
+ if (kh_exist(idx->tname, k))
+ names[kh_val(idx->tname, k)] = kh_key(idx->tname, k);
+ return names;
+}
+
+ti_index_t *ti_index_load(const char *fn)
+{
+ ti_index_t *idx;
+ char *fname = get_local_version(fn);
+ if (fname == 0) return 0;
+ idx = ti_index_load_local(fname);
+ if (idx == 0) fprintf(pysamerr, "[ti_index_load] fail to load the index: %s\n", fname);
+ free(fname);
+ return idx;
+}
+
+int ti_index_build2(const char *fn, const ti_conf_t *conf, const char *_fnidx)
+{
+ char *fnidx;
+ BGZF *fp, *fpidx;
+ ti_index_t *idx;
+ if ((fp = bgzf_open(fn, "r")) == 0) {
+ fprintf(pysamerr, "[ti_index_build2] fail to open the file: %s\n", fn);
+ return -1;
+ }
+ idx = ti_index_core(fp, conf);
+ bgzf_close(fp);
+ if (_fnidx == 0) {
+ fnidx = (char*)calloc(strlen(fn) + 5, 1);
+ strcpy(fnidx, fn); strcat(fnidx, ".tbi");
+ } else fnidx = strdup(_fnidx);
+ fpidx = bgzf_open(fnidx, "w");
+ if (fpidx == 0) {
+ fprintf(pysamerr, "[ti_index_build2] fail to create the index file.\n");
+ free(fnidx);
+ return -1;
+ }
+ ti_index_save(idx, fpidx);
+ ti_index_destroy(idx);
+ bgzf_close(fpidx);
+ free(fnidx);
+ return 0;
+}
+
+int ti_index_build(const char *fn, const ti_conf_t *conf)
+{
+ return ti_index_build2(fn, conf, 0);
+}
+
+/********************************************
+ * parse a region in the format chr:beg-end *
+ ********************************************/
+
+int ti_get_tid(const ti_index_t *idx, const char *name)
+{
+ khiter_t iter;
+ const khash_t(s) *h = idx->tname;
+ iter = kh_get(s, h, name); /* get the tid */
+ if (iter == kh_end(h)) return -1;
+ return kh_value(h, iter);
+}
+
+int ti_parse_region(const ti_index_t *idx, const char *str, int *tid, int *begin, int *end)
+{
+ char *s, *p;
+ int i, l, k;
+ l = strlen(str);
+ p = s = (char*)malloc(l+1);
+ /* squeeze out "," */
+ for (i = k = 0; i != l; ++i)
+ if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
+ s[k] = 0;
+ for (i = 0; i != k; ++i) if (s[i] == ':') break;
+ s[i] = 0;
+ if ((*tid = ti_get_tid(idx, s)) < 0) {
+ free(s);
+ return -1;
+ }
+ if (i == k) { /* dump the whole sequence */
+ *begin = 0; *end = 1<<29; free(s);
+ return 0;
+ }
+ for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
+ *begin = atoi(p);
+ if (i < k) {
+ p = s + i + 1;
+ *end = atoi(p);
+ } else *end = 1<<29;
+ if (*begin > 0) --*begin;
+ free(s);
+ if (*begin > *end) return -1;
+ return 0;
+}
+
+/*******************************
+ * retrieve a specified region *
+ *******************************/
+
+#define MAX_BIN 37450 // =(8^6-1)/7+1
+
+static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[MAX_BIN])
+{
+ int i = 0, k;
+ if (beg >= end) return 0;
+ if (end >= 1u<<29) end = 1u<<29;
+ --end;
+ list[i++] = 0;
+ for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k;
+ for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) list[i++] = k;
+ for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) list[i++] = k;
+ for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) list[i++] = k;
+ for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k;
+ return i;
+}
+
+ti_iter_t ti_iter_first()
+{
+ ti_iter_t iter;
+ iter = calloc(1, sizeof(struct __ti_iter_t));
+ iter->from_first = 1;
+ return iter;
+}
+
+ti_iter_t ti_iter_query(const ti_index_t *idx, int tid, int beg, int end)
+{
+ uint16_t *bins;
+ int i, n_bins, n_off;
+ pair64_t *off;
+ khint_t k;
+ khash_t(i) *index;
+ uint64_t min_off;
+ ti_iter_t iter = 0;
+
+ if (beg < 0) beg = 0;
+ if (end < beg) return 0;
+ // initialize the iterator
+ iter = calloc(1, sizeof(struct __ti_iter_t));
+ iter->idx = idx; iter->tid = tid; iter->beg = beg; iter->end = end; iter->i = -1;
+ // random access
+ bins = (uint16_t*)calloc(MAX_BIN, 2);
+ n_bins = reg2bins(beg, end, bins);
+ index = idx->index[tid];
+ if (idx->index2[tid].n > 0) {
+ min_off = (beg>>TAD_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1]
+ : idx->index2[tid].offset[beg>>TAD_LIDX_SHIFT];
+ if (min_off == 0) { // improvement for index files built by tabix prior to 0.1.4
+ int n = beg>>TAD_LIDX_SHIFT;
+ if (n > idx->index2[tid].n) n = idx->index2[tid].n;
+ for (i = n - 1; i >= 0; --i)
+ if (idx->index2[tid].offset[i] != 0) break;
+ if (i >= 0) min_off = idx->index2[tid].offset[i];
+ }
+ } else min_off = 0; // tabix 0.1.2 may produce such index files
+ for (i = n_off = 0; i < n_bins; ++i) {
+ if ((k = kh_get(i, index, bins[i])) != kh_end(index))
+ n_off += kh_value(index, k).n;
+ }
+ if (n_off == 0) {
+ free(bins); return iter;
+ }
+ off = (pair64_t*)calloc(n_off, 16);
+ for (i = n_off = 0; i < n_bins; ++i) {
+ if ((k = kh_get(i, index, bins[i])) != kh_end(index)) {
+ int j;
+ ti_binlist_t *p = &kh_value(index, k);
+ for (j = 0; j < p->n; ++j)
+ if (p->list[j].v > min_off) off[n_off++] = p->list[j];
+ }
+ }
+ if (n_off == 0) {
+ free(bins); free(off); return iter;
+ }
+ free(bins);
+ {
+ int l;
+ ks_introsort(offt, n_off, off);
+ // resolve completely contained adjacent blocks
+ for (i = 1, l = 0; i < n_off; ++i)
+ if (off[l].v < off[i].v)
+ off[++l] = off[i];
+ n_off = l + 1;
+ // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing
+ for (i = 1; i < n_off; ++i)
+ if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u;
+ { // merge adjacent blocks
+ for (i = 1, l = 0; i < n_off; ++i) {
+ if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v;
+ else off[++l] = off[i];
+ }
+ n_off = l + 1;
+ }
+ }
+ iter->n_off = n_off; iter->off = off;
+ return iter;
+}
+
+const char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
+{
+ if (iter->finished) return 0;
+ if (iter->from_first) {
+ int ret;
+ if ((ret = ti_readline(fp, &iter->str)) < 0) {
+ iter->finished = 1;
+ return 0;
+ } else {
+ if (len) *len = iter->str.l;
+ return iter->str.s;
+ }
+ }
+ if (iter->n_off == 0) return 0;
+ while (1) {
+ int ret;
+ if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk
+ if (iter->i == iter->n_off - 1) break; // no more chunks
+ if (iter->i >= 0) assert(iter->curr_off == iter->off[iter->i].v); // otherwise bug
+ if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek
+ bgzf_seek(fp, iter->off[iter->i+1].u, SEEK_SET);
+ iter->curr_off = bgzf_tell(fp);
+ }
+ ++iter->i;
+ }
+ if ((ret = ti_readline(fp, &iter->str)) >= 0) {
+ ti_intv_t intv;
+ iter->curr_off = bgzf_tell(fp);
+ if (iter->str.s[0] == iter->idx->conf.meta_char) continue;
+ get_intv((ti_index_t*)iter->idx, &iter->str, &intv);
+ if (intv.tid != iter->tid || intv.beg >= iter->end) break; // no need to proceed
+ else if (intv.end > iter->beg && iter->end > intv.beg) {
+ if (len) *len = iter->str.l;
+ return iter->str.s;
+ }
+ } else break; // end of file
+ }
+ iter->finished = 1;
+ return 0;
+}
+
+void ti_iter_destroy(ti_iter_t iter)
+{
+ if (iter) {
+ free(iter->str.s); free(iter->off);
+ free(iter);
+ }
+}
+
+int ti_fetch(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end, void *data, ti_fetch_f func)
+{
+ ti_iter_t iter;
+ const char *s;
+ int len;
+ iter = ti_iter_query(idx, tid, beg, end);
+ while ((s = ti_iter_read(fp, iter, &len)) != 0)
+ func(len, s, data);
+ ti_iter_destroy(iter);
+ return 0;
+}
+
+const ti_conf_t *ti_get_conf(ti_index_t *idx) { return idx? &idx->conf : 0; }
+
+/*******************
+ * High-level APIs *
+ *******************/
+
+tabix_t *ti_open(const char *fn, const char *fnidx)
+{
+ tabix_t *t;
+ BGZF *fp;
+ if ((fp = bgzf_open(fn, "r")) == 0) return 0;
+ t = calloc(1, sizeof(tabix_t));
+ t->fn = strdup(fn);
+ if (fnidx) t->fnidx = strdup(fnidx);
+ t->fp = fp;
+ return t;
+}
+
+void ti_close(tabix_t *t)
+{
+ if (t) {
+ bgzf_close(t->fp);
+ if (t->idx) ti_index_destroy(t->idx);
+ free(t->fn); free(t->fnidx);
+ free(t);
+ }
+}
+
+int ti_lazy_index_load(tabix_t *t)
+{
+ if (t->idx == 0) { // load index
+ if (t->fnidx) t->idx = ti_index_load_local(t->fnidx);
+ else t->idx = ti_index_load(t->fn);
+ if (t->idx == 0) return -1; // fail to load index
+ }
+ return 0;
+}
+
+ti_iter_t ti_queryi(tabix_t *t, int tid, int beg, int end)
+{
+ if (tid < 0) return ti_iter_first();
+ if (ti_lazy_index_load(t) != 0) return 0;
+ return ti_iter_query(t->idx, tid, beg, end);
+}
+
+ti_iter_t ti_querys(tabix_t *t, const char *reg)
+{
+ int tid, beg, end;
+ if (reg == 0) return ti_iter_first();
+ if (ti_lazy_index_load(t) != 0) return 0;
+ if (ti_parse_region(t->idx, reg, &tid, &beg, &end) < 0) return 0;
+ return ti_iter_query(t->idx, tid, beg, end);
+}
+
+ti_iter_t ti_query(tabix_t *t, const char *name, int beg, int end)
+{
+ int tid;
+ if (name == 0) return ti_iter_first();
+ // then need to load the index
+ if (ti_lazy_index_load(t) != 0) return 0;
+ if ((tid = ti_get_tid(t->idx, name)) < 0) return 0;
+ return ti_iter_query(t->idx, tid, beg, end);
+}
+
+const char *ti_read(tabix_t *t, ti_iter_t iter, int *len)
+{
+ return ti_iter_read(t->fp, iter, len);
+}
projects / pysam.git / blobdiff