move bcftools to samtools

[samtools.git] / bam_index.c

diff --git a/bam_index.c b/bam_index.c
index 6fffd75e1ed5c58c363847abd42fed04e638c5b0..4152f2022f3178ef4fd0ee6b6001effae8f2ce3c 100644 (file)
--- a/bam_index.c
+++ b/bam_index.c
@@ -42,6 +42,8 @@
 // 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;
@@ -63,6 +65,7 @@ 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;
 };
@@ -117,7 +120,7 @@ static void merge_chunks(bam_index_t *idx)
                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) {
@@ -154,7 +157,7 @@ bam_index_t *bam_index_core(bamFile fp)
        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));
@@ -169,7 +172,10 @@ bam_index_t *bam_index_core(bamFile fp)
 
        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;
@@ -178,10 +184,17 @@ bam_index_t *bam_index_core(bamFile fp)
                                        bam1_qname(b), last_coor, c->pos, c->tid+1);
                        exit(1);
                }
-               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;
@@ -192,14 +205,23 @@ bam_index_t *bam_index_core(bamFile fp)
                                        (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, off_end);
+               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 (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;
 }
 
@@ -277,6 +299,11 @@ void bam_index_save(const bam_index_t *idx, FILE *fp)
                                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);
 }
 
@@ -338,6 +365,8 @@ static bam_index_t *bam_index_load_core(FILE *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;
 }
 
@@ -462,7 +491,7 @@ int bam_index_build(const char *fn)
 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]);
@@ -470,9 +499,39 @@ int bam_index(int argc, char *argv[])
        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;
@@ -518,7 +577,7 @@ bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end)
        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) {