// 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;
struct __bam_index_t {
int32_t n;
+ uint64_t n_no_coor; // unmapped reads without coordinate
khash_t(i) **index;
bam_lidx_t *index2;
};
index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
memset(index2->offset + old_m, 0, 8 * (index2->m - old_m));
}
- for (i = beg + 1; i <= end; ++i)
- if (index2->offset[i] == 0) index2->offset[i] = offset;
+ 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;
}
index = idx->index[i];
for (k = kh_begin(index); k != kh_end(index); ++k) {
bam_binlist_t *p;
- if (!kh_exist(index, k)) continue;
+ 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) {
#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;
uint32_t last_bin, save_bin;
int32_t last_coor, last_tid, save_tid;
bam1_core_t *c;
- uint64_t save_off, last_off;
+ 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));
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;
bam1_qname(b), last_coor, c->pos, c->tid+1);
exit(1);
}
- if (b->core.tid >= 0 && b->core.bin < 4681) insert_offset2(&idx->index2[b->core.tid], b, last_off);
+ 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;
(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));
+ 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(stderr, "[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.\n");
+ exit(1);
+ }
+ }
+ }
if (ret < -1) fprintf(stderr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret);
free(b->data); free(b);
+ idx->n_no_coor = n_no_coor;
return idx;
}
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);
}
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;
}
} else fn = strdup(_fn);
fnidx = (char*)calloc(strlen(fn) + 5, 1);
strcpy(fnidx, fn); strcat(fnidx, ".bai");
- fp = fopen(fnidx, "r");
+ 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, "r");
+ fp = fopen(fnidx, "rb");
}
}
free(fnidx); free(fn);
fprintf(stderr, "[download_from_remote] fail to open remote file.\n");
return;
}
- if ((fp = fopen(fn, "w")) == 0) {
+ if ((fp = fopen(fn, "wb")) == 0) {
fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n");
knet_close(fp_remote);
return;
fnidx = (char*)calloc(strlen(fn) + 5, 1);
strcpy(fnidx, fn); strcat(fnidx, ".bai");
} else fnidx = strdup(_fnidx);
- fpidx = fopen(fnidx, "w");
+ fpidx = fopen(fnidx, "wb");
if (fpidx == 0) {
fprintf(stderr, "[bam_index_build2] fail to create the index file.\n");
free(fnidx);
int bam_index(int argc, char *argv[])
{
if (argc < 2) {
- fprintf(stderr, "Usage: samtools index <in.bam> [<out.index>]\n");
+ fprintf(stderr, "Usage: samtools index <in.bam> [out.index]\n");
return 1;
}
if (argc >= 3) bam_index_build2(argv[1], argv[2]);
return 0;
}
-#define MAX_BIN 37450 // =(8^6-1)/7+1
+int bam_idxstats(int argc, char *argv[])
+{
+ bam_index_t *idx;
+ bam_header_t *header;
+ bamFile fp;
+ int i;
+ if (argc < 2) {
+ fprintf(stderr, "Usage: samtools idxstats <in.bam>\n");
+ return 1;
+ }
+ fp = bam_open(argv[1], "r");
+ if (fp == 0) { fprintf(stderr, "[%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(stderr, "[%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[MAX_BIN])
+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;
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
-pair64_t * get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int end, int* cnt_off)
+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;
khint_t k;
khash_t(i) *index;
uint64_t min_off;
-
- bins = (uint16_t*)calloc(MAX_BIN, 2);
+ 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];
- min_off = (beg>>BAM_LIDX_SHIFT >= idx->index2[tid].n)? 0 : idx->index2[tid].offset[beg>>BAM_LIDX_SHIFT];
+ 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 0;
+ free(bins); return iter;
}
off = (pair64_t*)calloc(n_off, 16);
for (i = n_off = 0; i < n_bins; ++i) {
}
}
free(bins);
+ if (n_off == 0) {
+ free(off); return iter;
+ }
{
bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
int l;
}
bam_destroy1(b);
}
- *cnt_off = n_off;
+ 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;
}
-int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
+void bam_iter_destroy(bam_iter_t iter)
{
- int n_off;
- pair64_t *off = get_chunk_coordinates(idx, tid, beg, end, &n_off);
- if (off == 0) return 0;
- {
- // retrive alignments
- uint64_t curr_off;
- int i, ret, n_seeks;
- n_seeks = 0; i = -1; curr_off = 0;
- bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
- for (;;) {
- if (curr_off == 0 || curr_off >= off[i].v) { // then jump to the next chunk
- if (i == n_off - 1) break; // no more chunks
- if (i >= 0) assert(curr_off == off[i].v); // otherwise bug
- if (i < 0 || off[i].v != off[i+1].u) { // not adjacent chunks; then seek
- bam_seek(fp, off[i+1].u, SEEK_SET);
- curr_off = bam_tell(fp);
- ++n_seeks;
- }
- ++i;
+ 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);
}
- if ((ret = bam_read1(fp, b)) > 0) {
- curr_off = bam_tell(fp);
- if (b->core.tid != tid || b->core.pos >= end) break; // no need to proceed
- else if (is_overlap(beg, end, b)) func(b, data);
- } else break; // end of file
+ ++iter->i;
}
-// fprintf(stderr, "[bam_fetch] # seek calls: %d\n", n_seeks);
- bam_destroy1(b);
+ 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
}
- free(off);
- return 0;
+ 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 / samtools.git / blobdiff