* samtools-0.1.7-15 (r592)

[samtools.git] / bam_index.c

diff --git a/bam_index.c b/bam_index.c
index 0d3e6fe8aca611b73b83bcb3fb7bdafd087f6753..595ef047733dc62282732c0dd6ece2d29537887f 100644 (file)
--- a/bam_index.c
+++ b/bam_index.c
@@ -475,6 +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;
@@ -496,7 +498,6 @@ struct __bam_iterf_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;
 };
 
@@ -515,7 +516,7 @@ bam_iterf_t bam_iterf_query(const bam_index_t *idx, int tid, int beg, int end)
        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->tid = tid, iter->beg = beg, iter->end = end; iter->i = -1;
        //
        bins = (uint16_t*)calloc(MAX_BIN, 2);
        n_bins = reg2bins(beg, end, bins);