// 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;
};
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) {
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;
+
+ h = bam_header_read(fp);
+ if(h == 0) {
+ fprintf(stderr, "[bam_index_core] Invalid BAM header.");
+ return NULL;
+ }
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;
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 (last_tid != c->tid) { // change of chromosomes
+ if (c->tid < 0) ++n_no_coor;
+ if (last_tid < c->tid || (last_tid >= 0 && c->tid < 0)) { // change of chromosomes
last_tid = c->tid;
last_bin = 0xffffffffu;
- } else if (last_coor > c->pos) {
+ } else if ((uint32_t)last_tid > (uint32_t)c->tid) {
+ fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %d-th chr > %d-th chr\n",
+ bam1_qname(b), last_tid+1, c->tid+1);
+ return NULL;
+ } else if ((int32_t)c->tid >= 0 && last_coor > c->pos) {
fprintf(stderr, "[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);
+ return NULL;
}
- insert_offset2(&idx->index2[b->core.tid], b, last_off);
+ if (c->tid >= 0 && !(c->flag & BAM_FUNMAP)) 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 (bam_tell(fp) <= last_off) {
fprintf(stderr, "[bam_index_core] bug in BGZF/RAZF: %llx < %llx\n",
(unsigned long long)bam_tell(fp), (unsigned long long)last_off);
- exit(1);
+ return NULL;
}
+ 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");
+ return NULL;
+ }
+ }
+ }
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;
}
}
idx = bam_index_core(fp);
bam_close(fp);
+ if(idx == 0) {
+ fprintf(stderr, "[bam_index_build2] fail to index the BAM file.\n");
+ return -1;
+ }
if (_fnidx == 0) {
fnidx = (char*)calloc(strlen(fn) + 5, 1);
strcpy(fnidx, fn); strcat(fnidx, ".bai");
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;
iter = calloc(1, sizeof(struct __bam_iter_t));
iter->tid = tid, iter->beg = beg, iter->end = end; iter->i = -1;
//
- bins = (uint16_t*)calloc(MAX_BIN, 2);
+ bins = (uint16_t*)calloc(BAM_MAX_BIN, 2);
n_bins = reg2bins(beg, end, bins);
index = idx->index[tid];
if (idx->index2[tid].n > 0) {
}
}
free(bins);
+ if (n_off == 0) {
+ free(off); return iter;
+ }
{
bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
int l;
int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b)
{
- if (iter->finished) return -1;
- if (iter->from_first) {
- int ret = bam_read1(fp, b);
- if (ret < 0) iter->finished = 1;
+ 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 (;;) {
- 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 == 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->i;
}
- if ((ret = bam_read1(fp, b)) > 0) {
+ if ((ret = bam_read1(fp, b)) >= 0) {
iter->curr_off = bam_tell(fp);
- if (b->core.tid != iter->tid || b->core.pos >= iter->end) break; // no need to proceed
+ 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
+ } else break; // end of file or error
}
iter->finished = 1;
- return -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 (bam_iter_read(fp, iter, b) >= 0) func(b, data);
+ while ((ret = bam_iter_read(fp, iter, b)) >= 0) func(b, data);
+ bam_iter_destroy(iter);
bam_destroy1(b);
- return 0;
+ return (ret == -1)? 0 : ret;
}
projects / samtools.git / blobdiff