* samtools-0.1.6-9 (r469)

 * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.

diff --git a/bam_index.c b/bam_index.c
index 4ff6bd482505172741c5a48ab413f141342e93bc..4606d6b1107f1c901d5961be1309e0c87e69d674 100644 (file)
--- a/bam_index.c
+++ b/bam_index.c
@@ -476,7 +476,8 @@ static inline int is_overlap(uint32_t beg, uint32_t end, const bam1_t *b)
        return (rend > beg && rbeg < end);
 }
 
-int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
+// bam_fetch helper function retrieves 
+pair64_t * get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int end, int* cnt_off)
 {
        uint16_t *bins;
        int i, n_bins, n_off;
@@ -507,10 +508,8 @@ int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, voi
        }
        free(bins);
        {
-               bam1_t *b;
-               int l, ret, n_seeks;
-               uint64_t curr_off;
-               b = (bam1_t*)calloc(1, sizeof(bam1_t));
+               bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
+               int l;
                ks_introsort(off, n_off, off);
                // resolve completely contained adjacent blocks
                for (i = 1, l = 0; i < n_off; ++i)
@@ -533,8 +532,22 @@ int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, voi
                        n_off = l + 1;
 #endif
                }
+               bam_destroy1(b);
+       }
+       *cnt_off = n_off;
+       return off;
+}
+
+int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
+{
+       int n_off;
+       pair64_t *off = get_chunk_coordinates(idx, tid, beg, end, &n_off);
+       {
                // retrive alignments
+               uint64_t curr_off;
+               int i, ret, n_seeks;
                n_seeks = 0; i = -1; curr_off = 0;
+               bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
                for (;;) {
                        if (curr_off == 0 || curr_off >= off[i].v) { // then jump to the next chunk
                                if (i == n_off - 1) break; // no more chunks

diff --git a/bamtk.c b/bamtk.c
index b824c1ecd29102cb7fd50d79d9d3b39312d72ee4..ae8f607bbf86475d260cf90e8d1bea3ce592dbc0 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.6-7 (r468)"
+#define PACKAGE_VERSION "0.1.6-8 (r469)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);