* samtools-0.1.8-7 (r639)

[samtools.git] / bam_index.c

diff --git a/bam_index.c b/bam_index.c
index 074f918752209e90f50b9082f9bb93e5f4a7f2af..4152f2022f3178ef4fd0ee6b6001effae8f2ce3c 100644 (file)
--- a/bam_index.c
+++ b/bam_index.c
@@ -65,6 +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;
 };
@@ -119,7 +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) {
@@ -156,7 +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, n_mapped, n_unmapped, off_beg, off_end;
+       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));
@@ -171,9 +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 = off_end = 0;
+    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;
@@ -208,11 +210,18 @@ bam_index_t *bam_index_core(bamFile fp)
                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;
 }
 
@@ -290,6 +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);
 }
 
@@ -351,6 +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;
 }
 
@@ -506,8 +522,10 @@ int bam_idxstats(int argc, char *argv[])
                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;