rename iterf as iter

[samtools.git] / bam_index.c

diff --git a/bam_index.c b/bam_index.c
index 570d64585af202fd334251034fa773f388e9aff3..6fffd75e1ed5c58c363847abd42fed04e638c5b0 100644 (file)
--- a/bam_index.c
+++ b/bam_index.c
@@ -98,8 +98,12 @@ static inline void insert_offset2(bam_lidx_t *index2, bam1_t *b, uint64_t offset
                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;
 }
 
@@ -130,6 +134,17 @@ static void merge_chunks(bam_index_t *idx)
 #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;
@@ -163,7 +178,7 @@ bam_index_t *bam_index_core(bamFile fp)
                                        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);
+               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);
@@ -182,6 +197,7 @@ bam_index_t *bam_index_core(bamFile fp)
        }
        if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
        merge_chunks(idx);
+       fill_missing(idx);
        if (ret < -1) fprintf(stderr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret);
        free(b->data); free(b);
        return idx;
@@ -459,6 +475,8 @@ int bam_index(int argc, char *argv[])
 static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[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;
@@ -476,16 +494,15 @@ static inline int is_overlap(uint32_t beg, uint32_t end, const bam1_t *b)
        return (rend > beg && rbeg < end);
 }
 
-struct __bam_iterf_t {
+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;
-       const bam_index_t *idx;
        pair64_t *off;
 };
 
 // bam_fetch helper function retrieves 
-bam_iterf_t bam_iterf_query(const bam_index_t *idx, int tid, int beg, int end)
+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;
@@ -493,18 +510,28 @@ bam_iterf_t bam_iterf_query(const bam_index_t *idx, int tid, int beg, int end)
        khint_t k;
        khash_t(i) *index;
        uint64_t min_off;
-       bam_iterf_t iter = 0;
+       bam_iter_t iter = 0;
 
        if (beg < 0) beg = 0;
        if (end < beg) return 0;
        // initialize iter
-       iter = calloc(1, sizeof(struct __bam_iterf_t));
-       iter->idx = idx; iter->tid = tid, iter->beg = beg, iter->end = end; iter->i = -1;
+       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);
        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;
@@ -555,20 +582,20 @@ bam_iterf_t bam_iterf_query(const bam_index_t *idx, int tid, int beg, int end)
 
 pair64_t *get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int end, int *cnt_off)
 { // for pysam compatibility
-       bam_iterf_t iter;
+       bam_iter_t iter;
        pair64_t *off;
-       iter = bam_iterf_query(idx, tid, beg, end);
+       iter = bam_iter_query(idx, tid, beg, end);
        off = iter->off; *cnt_off = iter->n_off;
        free(iter);
        return off;
 }
 
-void bam_iterf_destroy(bam_iterf_t iter)
+void bam_iter_destroy(bam_iter_t iter)
 {
        if (iter) { free(iter->off); free(iter); }
 }
 
-int bam_iterf_read(bamFile fp, bam_iterf_t iter, bam1_t *b)
+int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b)
 {
        if (iter->finished) return -1;
        if (iter->from_first) {
@@ -600,11 +627,11 @@ int bam_iterf_read(bamFile fp, bam_iterf_t iter, bam1_t *b)
 
 int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
 {
-       bam_iterf_t iter;
+       bam_iter_t iter;
        bam1_t *b;
        b = bam_init1();
-       iter = bam_iterf_query(idx, tid, beg, end);
-       while (bam_iterf_read(fp, iter, b) >= 0) func(b, data);
+       iter = bam_iter_query(idx, tid, beg, end);
+       while (bam_iter_read(fp, iter, b) >= 0) func(b, data);
        bam_destroy1(b);
        return 0;
 }