--- /dev/null
+#include "pysam.h"
+
+#include <ctype.h>
+#include <assert.h>
+#include "bam.h"
+#include "khash.h"
+#include "ksort.h"
+#include "bam_endian.h"
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+
+/*!
+ @header
+
+ Alignment indexing. Before indexing, BAM must be sorted based on the
+ leftmost coordinate of alignments. In indexing, BAM uses two indices:
+ a UCSC binning index and a simple linear index. The binning index is
+ efficient for alignments spanning long distance, while the auxiliary
+ linear index helps to reduce unnecessary seek calls especially for
+ short alignments.
+
+ The UCSC binning scheme was suggested by Richard Durbin and Lincoln
+ Stein and is explained by Kent et al. (2002). In this scheme, each bin
+ represents a contiguous genomic region which can be fully contained in
+ another bin; each alignment is associated with a bin which represents
+ the smallest region containing the entire alignment. The binning
+ scheme is essentially another representation of R-tree. A distinct bin
+ uniquely corresponds to a distinct internal node in a R-tree. Bin A is
+ a child of Bin B if region A is contained in B.
+
+ In BAM, each bin may span 2^29, 2^26, 2^23, 2^20, 2^17 or 2^14 bp. Bin
+ 0 spans a 512Mbp region, bins 1-8 span 64Mbp, 9-72 8Mbp, 73-584 1Mbp,
+ 585-4680 128Kbp and bins 4681-37449 span 16Kbp regions. If we want to
+ find the alignments overlapped with a region [rbeg,rend), we need to
+ calculate the list of bins that may be overlapped the region and test
+ the alignments in the bins to confirm the overlaps. If the specified
+ region is short, typically only a few alignments in six bins need to
+ be retrieved. The overlapping alignments can be quickly fetched.
+
+ */
+
+#define BAM_MIN_CHUNK_GAP 32768
+// 1<<14 is the size of minimum bin.
+#define BAM_LIDX_SHIFT 14
+
+#define BAM_MAX_BIN 37450 // =(8^6-1)/7+1
+
+typedef struct {
+ uint64_t u, v;
+} pair64_t;
+
+#define pair64_lt(a,b) ((a).u < (b).u)
+KSORT_INIT(off, pair64_t, pair64_lt)
+
+typedef struct {
+ uint32_t m, n;
+ pair64_t *list;
+} bam_binlist_t;
+
+typedef struct {
+ int32_t n, m;
+ uint64_t *offset;
+} bam_lidx_t;
+
+KHASH_MAP_INIT_INT(i, bam_binlist_t)
+
+struct __bam_index_t {
+ int32_t n;
+ uint64_t n_no_coor; // unmapped reads without coordinate
+ khash_t(i) **index;
+ bam_lidx_t *index2;
+};
+
+// requirement: len <= LEN_MASK
+static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t end)
+{
+ khint_t k;
+ bam_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 void insert_offset2(bam_lidx_t *index2, bam1_t *b, uint64_t offset)
+{
+ int i, beg, end;
+ beg = b->core.pos >> BAM_LIDX_SHIFT;
+ end = (bam_calend(&b->core, bam1_cigar(b)) - 1) >> BAM_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;
+ }
+ index2->n = end + 1;
+}
+
+static void merge_chunks(bam_index_t *idx)
+{
+#if defined(BAM_TRUE_OFFSET) || defined(BAM_VIRTUAL_OFFSET16)
+ 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) {
+ bam_binlist_t *p;
+ if (!kh_exist(index, k) || kh_key(index, k) == BAM_MAX_BIN) continue;
+ p = &kh_value(index, k);
+ m = 0;
+ for (l = 1; l < p->n; ++l) {
+#ifdef BAM_TRUE_OFFSET
+ if (p->list[m].v + BAM_MIN_CHUNK_GAP > p->list[l].u) p->list[m].v = p->list[l].v;
+#else
+ if (p->list[m].v>>16 == p->list[l].u>>16) p->list[m].v = p->list[l].v;
+#endif
+ else p->list[++m] = p->list[l];
+ } // ~for(l)
+ p->n = m + 1;
+ } // ~for(k)
+ } // ~for(i)
+#endif // defined(BAM_TRUE_OFFSET) || defined(BAM_BGZF)
+}
+
+static void fill_missing(bam_index_t *idx)
+{
+ int i, j;
+ for (i = 0; i < idx->n; ++i) {
+ bam_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];
+ }
+}
+
+bam_index_t *bam_index_core(bamFile fp)
+{
+ bam1_t *b;
+ bam_header_t *h;
+ int i, ret;
+ bam_index_t *idx;
+ uint32_t last_bin, save_bin;
+ int32_t last_coor, last_tid, save_tid;
+ bam1_core_t *c;
+ uint64_t save_off, last_off, n_mapped, n_unmapped, off_beg, off_end, n_no_coor;
+
+ idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
+ b = (bam1_t*)calloc(1, sizeof(bam1_t));
+ h = bam_header_read(fp);
+ c = &b->core;
+
+ idx->n = h->n_targets;
+ bam_header_destroy(h);
+ idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
+ for (i = 0; i < idx->n; ++i) idx->index[i] = kh_init(i);
+ idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t));
+
+ save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
+ save_off = last_off = bam_tell(fp); last_coor = 0xffffffffu;
+ n_mapped = n_unmapped = n_no_coor = off_end = 0;
+ off_beg = off_end = bam_tell(fp);
+ while ((ret = bam_read1(fp, b)) >= 0) {
+ if (c->tid < 0) ++n_no_coor;
+ if (last_tid != c->tid) { // change of chromosomes
+ last_tid = c->tid;
+ last_bin = 0xffffffffu;
+ } else if (last_coor > c->pos) {
+ fprintf(pysamerr, "[bam_index_core] the alignment is not sorted (%s): %u > %u in %d-th chr\n",
+ bam1_qname(b), last_coor, c->pos, c->tid+1);
+ exit(1);
+ }
+ if (c->tid >= 0) insert_offset2(&idx->index2[b->core.tid], b, last_off);
+ if (c->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);
+ if (last_bin == 0xffffffffu && save_tid != 0xffffffffu) { // write the meta element
+ off_end = last_off;
+ insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, off_end);
+ insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped);
+ n_mapped = n_unmapped = 0;
+ off_beg = off_end;
+ }
+ save_off = last_off;
+ save_bin = last_bin = c->bin;
+ save_tid = c->tid;
+ if (save_tid < 0) break;
+ }
+ if (bam_tell(fp) <= last_off) {
+ fprintf(pysamerr, "[bam_index_core] bug in BGZF/RAZF: %llx < %llx\n",
+ (unsigned long long)bam_tell(fp), (unsigned long long)last_off);
+ exit(1);
+ }
+ if (c->flag & BAM_FUNMAP) ++n_unmapped;
+ else ++n_mapped;
+ last_off = bam_tell(fp);
+ last_coor = b->core.pos;
+ }
+ if (save_tid >= 0) {
+ insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
+ insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, bam_tell(fp));
+ insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped);
+ }
+ merge_chunks(idx);
+ fill_missing(idx);
+ if (ret >= 0) {
+ while ((ret = bam_read1(fp, b)) >= 0) {
+ ++n_no_coor;
+ if (c->tid >= 0 && n_no_coor) {
+ fprintf(pysamerr, "[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.\n");
+ exit(1);
+ }
+ }
+ }
+ if (ret < -1) fprintf(pysamerr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret);
+ free(b->data); free(b);
+ idx->n_no_coor = n_no_coor;
+ return idx;
+}
+
+void bam_index_destroy(bam_index_t *idx)
+{
+ khint_t k;
+ int i;
+ if (idx == 0) return;
+ for (i = 0; i < idx->n; ++i) {
+ khash_t(i) *index = idx->index[i];
+ bam_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); free(idx->index2);
+ free(idx);
+}
+
+void bam_index_save(const bam_index_t *idx, FILE *fp)
+{
+ int32_t i, size;
+ khint_t k;
+ fwrite("BAI\1", 1, 4, fp);
+ if (bam_is_be) {
+ uint32_t x = idx->n;
+ fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
+ } else fwrite(&idx->n, 4, 1, fp);
+ for (i = 0; i < idx->n; ++i) {
+ khash_t(i) *index = idx->index[i];
+ bam_lidx_t *index2 = idx->index2 + i;
+ // write binning index
+ size = kh_size(index);
+ if (bam_is_be) { // big endian
+ uint32_t x = size;
+ fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
+ } else fwrite(&size, 4, 1, fp);
+ for (k = kh_begin(index); k != kh_end(index); ++k) {
+ if (kh_exist(index, k)) {
+ bam_binlist_t *p = &kh_value(index, k);
+ if (bam_is_be) { // big endian
+ uint32_t x;
+ x = kh_key(index, k); fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
+ x = p->n; fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
+ for (x = 0; (int)x < p->n; ++x) {
+ bam_swap_endian_8p(&p->list[x].u);
+ bam_swap_endian_8p(&p->list[x].v);
+ }
+ fwrite(p->list, 16, p->n, fp);
+ 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 {
+ fwrite(&kh_key(index, k), 4, 1, fp);
+ fwrite(&p->n, 4, 1, fp);
+ fwrite(p->list, 16, p->n, fp);
+ }
+ }
+ }
+ // write linear index (index2)
+ if (bam_is_be) {
+ int x = index2->n;
+ fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
+ } else fwrite(&index2->n, 4, 1, fp);
+ if (bam_is_be) { // big endian
+ int x;
+ for (x = 0; (int)x < index2->n; ++x)
+ bam_swap_endian_8p(&index2->offset[x]);
+ fwrite(index2->offset, 8, index2->n, fp);
+ for (x = 0; (int)x < index2->n; ++x)
+ bam_swap_endian_8p(&index2->offset[x]);
+ } else fwrite(index2->offset, 8, index2->n, fp);
+ }
+ { // write the number of reads coor-less records.
+ uint64_t x = idx->n_no_coor;
+ if (bam_is_be) bam_swap_endian_8p(&x);
+ fwrite(&x, 8, 1, fp);
+ }
+ fflush(fp);
+}
+
+static bam_index_t *bam_index_load_core(FILE *fp)
+{
+ int i;
+ char magic[4];
+ bam_index_t *idx;
+ if (fp == 0) {
+ fprintf(pysamerr, "[bam_index_load_core] fail to load index.\n");
+ return 0;
+ }
+ fread(magic, 1, 4, fp);
+ if (strncmp(magic, "BAI\1", 4)) {
+ fprintf(pysamerr, "[bam_index_load] wrong magic number.\n");
+ fclose(fp);
+ return 0;
+ }
+ idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
+ fread(&idx->n, 4, 1, fp);
+ if (bam_is_be) bam_swap_endian_4p(&idx->n);
+ idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
+ idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t));
+ for (i = 0; i < idx->n; ++i) {
+ khash_t(i) *index;
+ bam_lidx_t *index2 = idx->index2 + i;
+ uint32_t key, size;
+ khint_t k;
+ int j, ret;
+ bam_binlist_t *p;
+ index = idx->index[i] = kh_init(i);
+ // load binning index
+ fread(&size, 4, 1, fp);
+ if (bam_is_be) bam_swap_endian_4p(&size);
+ for (j = 0; j < (int)size; ++j) {
+ fread(&key, 4, 1, fp);
+ if (bam_is_be) bam_swap_endian_4p(&key);
+ k = kh_put(i, index, key, &ret);
+ p = &kh_value(index, k);
+ fread(&p->n, 4, 1, fp);
+ if (bam_is_be) bam_swap_endian_4p(&p->n);
+ p->m = p->n;
+ p->list = (pair64_t*)malloc(p->m * 16);
+ fread(p->list, 16, p->n, fp);
+ if (bam_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
+ fread(&index2->n, 4, 1, fp);
+ if (bam_is_be) bam_swap_endian_4p(&index2->n);
+ index2->m = index2->n;
+ index2->offset = (uint64_t*)calloc(index2->m, 8);
+ fread(index2->offset, index2->n, 8, fp);
+ if (bam_is_be)
+ for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
+ }
+ if (fread(&idx->n_no_coor, 8, 1, fp) == 0) idx->n_no_coor = 0;
+ if (bam_is_be) bam_swap_endian_8p(&idx->n_no_coor);
+ return idx;
+}
+
+bam_index_t *bam_index_load_local(const char *_fn)
+{
+ FILE *fp;
+ char *fnidx, *fn;
+
+ if (strstr(_fn, "ftp://") == _fn || strstr(_fn, "http://") == _fn) {
+ const char *p;
+ int l = strlen(_fn);
+ for (p = _fn + l - 1; p >= _fn; --p)
+ if (*p == '/') break;
+ fn = strdup(p + 1);
+ } else fn = strdup(_fn);
+ fnidx = (char*)calloc(strlen(fn) + 5, 1);
+ strcpy(fnidx, fn); strcat(fnidx, ".bai");
+ fp = fopen(fnidx, "rb");
+ if (fp == 0) { // try "{base}.bai"
+ char *s = strstr(fn, "bam");
+ if (s == fn + strlen(fn) - 3) {
+ strcpy(fnidx, fn);
+ fnidx[strlen(fn)-1] = 'i';
+ fp = fopen(fnidx, "rb");
+ }
+ }
+ free(fnidx); free(fn);
+ if (fp) {
+ bam_index_t *idx = bam_index_load_core(fp);
+ fclose(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, "wb")) == 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
+
+bam_index_t *bam_index_load(const char *fn)
+{
+ bam_index_t *idx;
+ idx = bam_index_load_local(fn);
+ if (idx == 0 && (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)) {
+ char *fnidx = calloc(strlen(fn) + 5, 1);
+ strcat(strcpy(fnidx, fn), ".bai");
+ fprintf(pysamerr, "[bam_index_load] attempting to download the remote index file.\n");
+ download_from_remote(fnidx);
+ idx = bam_index_load_local(fn);
+ }
+ if (idx == 0) fprintf(pysamerr, "[bam_index_load] fail to load BAM index.\n");
+ return idx;
+}
+
+int bam_index_build2(const char *fn, const char *_fnidx)
+{
+ char *fnidx;
+ FILE *fpidx;
+ bamFile fp;
+ bam_index_t *idx;
+ if ((fp = bam_open(fn, "r")) == 0) {
+ fprintf(pysamerr, "[bam_index_build2] fail to open the BAM file.\n");
+ return -1;
+ }
+ idx = bam_index_core(fp);
+ bam_close(fp);
+ if (_fnidx == 0) {
+ fnidx = (char*)calloc(strlen(fn) + 5, 1);
+ strcpy(fnidx, fn); strcat(fnidx, ".bai");
+ } else fnidx = strdup(_fnidx);
+ fpidx = fopen(fnidx, "wb");
+ if (fpidx == 0) {
+ fprintf(pysamerr, "[bam_index_build2] fail to create the index file.\n");
+ free(fnidx);
+ return -1;
+ }
+ bam_index_save(idx, fpidx);
+ bam_index_destroy(idx);
+ fclose(fpidx);
+ free(fnidx);
+ return 0;
+}
+
+int bam_index_build(const char *fn)
+{
+ return bam_index_build2(fn, 0);
+}
+
+int bam_index(int argc, char *argv[])
+{
+ if (argc < 2) {
+ fprintf(pysamerr, "Usage: samtools index <in.bam> [out.index]\n");
+ return 1;
+ }
+ if (argc >= 3) bam_index_build2(argv[1], argv[2]);
+ else bam_index_build(argv[1]);
+ return 0;
+}
+
+int bam_idxstats(int argc, char *argv[])
+{
+ bam_index_t *idx;
+ bam_header_t *header;
+ bamFile fp;
+ int i;
+ if (argc < 2) {
+ fprintf(pysamerr, "Usage: samtools idxstats <in.bam>\n");
+ return 1;
+ }
+ fp = bam_open(argv[1], "r");
+ if (fp == 0) { fprintf(pysamerr, "[%s] fail to open BAM.\n", __func__); return 1; }
+ header = bam_header_read(fp);
+ bam_close(fp);
+ idx = bam_index_load(argv[1]);
+ if (idx == 0) { fprintf(pysamerr, "[%s] fail to load the index.\n", __func__); return 1; }
+ for (i = 0; i < idx->n; ++i) {
+ khint_t k;
+ khash_t(i) *h = idx->index[i];
+ printf("%s\t%d", header->target_name[i], header->target_len[i]);
+ k = kh_get(i, h, BAM_MAX_BIN);
+ if (k != kh_end(h))
+ printf("\t%llu\t%llu", (long long)kh_val(h, k).list[1].u, (long long)kh_val(h, k).list[1].v);
+ else printf("\t0\t0");
+ putchar('\n');
+ }
+ printf("*\t0\t0\t%llu\n", (long long)idx->n_no_coor);
+ bam_header_destroy(header);
+ bam_index_destroy(idx);
+ return 0;
+}
+
+static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[BAM_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;
+}
+
+static inline int is_overlap(uint32_t beg, uint32_t end, const bam1_t *b)
+{
+ uint32_t rbeg = b->core.pos;
+ uint32_t rend = b->core.n_cigar? bam_calend(&b->core, bam1_cigar(b)) : b->core.pos + 1;
+ return (rend > beg && rbeg < end);
+}
+
+struct __bam_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;
+ pair64_t *off;
+};
+
+// bam_fetch helper function retrieves
+bam_iter_t bam_iter_query(const bam_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;
+ bam_iter_t iter = 0;
+
+ if (beg < 0) beg = 0;
+ if (end < beg) return 0;
+ // initialize iter
+ iter = calloc(1, sizeof(struct __bam_iter_t));
+ iter->tid = tid, iter->beg = beg, iter->end = end; iter->i = -1;
+ //
+ bins = (uint16_t*)calloc(BAM_MAX_BIN, 2);
+ n_bins = reg2bins(beg, end, bins);
+ index = idx->index[tid];
+ if (idx->index2[tid].n > 0) {
+ min_off = (beg>>BAM_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1]
+ : idx->index2[tid].offset[beg>>BAM_LIDX_SHIFT];
+ if (min_off == 0) { // improvement for index files built by tabix prior to 0.1.4
+ int n = beg>>BAM_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;
+ bam_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];
+ }
+ }
+ free(bins);
+ if (n_off == 0) {
+ free(off); return iter;
+ }
+ {
+ bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
+ int l;
+ ks_introsort(off, 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
+#if defined(BAM_TRUE_OFFSET) || defined(BAM_VIRTUAL_OFFSET16)
+ for (i = 1, l = 0; i < n_off; ++i) {
+#ifdef BAM_TRUE_OFFSET
+ if (off[l].v + BAM_MIN_CHUNK_GAP > off[i].u) off[l].v = off[i].v;
+#else
+ if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v;
+#endif
+ else off[++l] = off[i];
+ }
+ n_off = l + 1;
+#endif
+ }
+ bam_destroy1(b);
+ }
+ iter->n_off = n_off; iter->off = off;
+ return iter;
+}
+
+pair64_t *get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int end, int *cnt_off)
+{ // for pysam compatibility
+ bam_iter_t iter;
+ pair64_t *off;
+ iter = bam_iter_query(idx, tid, beg, end);
+ off = iter->off; *cnt_off = iter->n_off;
+ free(iter);
+ return off;
+}
+
+void bam_iter_destroy(bam_iter_t iter)
+{
+ if (iter) { free(iter->off); free(iter); }
+}
+
+int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b)
+{
+ int ret;
+ if (iter && iter->finished) return -1;
+ if (iter == 0 || iter->from_first) {
+ ret = bam_read1(fp, b);
+ if (ret < 0 && iter) iter->finished = 1;
+ return ret;
+ }
+ if (iter->off == 0) return -1;
+ for (;;) {
+ 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) { ret = -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
+ bam_seek(fp, iter->off[iter->i+1].u, SEEK_SET);
+ iter->curr_off = bam_tell(fp);
+ }
+ ++iter->i;
+ }
+ if ((ret = bam_read1(fp, b)) >= 0) {
+ iter->curr_off = bam_tell(fp);
+ if (b->core.tid != iter->tid || b->core.pos >= iter->end) { // no need to proceed
+ ret = bam_validate1(NULL, b)? -1 : -5; // determine whether end of region or error
+ break;
+ }
+ else if (is_overlap(iter->beg, iter->end, b)) return ret;
+ } else break; // end of file or error
+ }
+ iter->finished = 1;
+ return ret;
+}
+
+int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
+{
+ int ret;
+ bam_iter_t iter;
+ bam1_t *b;
+ b = bam_init1();
+ iter = bam_iter_query(idx, tid, beg, end);
+ while ((ret = bam_iter_read(fp, iter, b)) >= 0) func(b, data);
+ bam_iter_destroy(iter);
+ bam_destroy1(b);
+ return (ret == -1)? 0 : ret;
+}
projects / pysam.git / blobdiff