Imported Upstream version 0.2.3

[tabix.git] / index.c

diff --git a/index.c b/index.c
index 8eddcecb34bab21f8d4f6de7a88639f8c67d0358..4ed32c2c2f4c83f89c7882f028a084276d340c75 100644 (file)
--- a/index.c
+++ b/index.c
@@ -240,7 +240,7 @@ static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t
        l->list[l->n].u = beg; l->list[l->n++].v = end;
 }
 
-static inline void insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_t offset)
+static inline uint64_t insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_t offset)
 {
        int i, beg, end;
        beg = _beg >> TAD_LIDX_SHIFT;
@@ -259,6 +259,7 @@ static inline void insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_
                        if (index2->offset[i] == 0) index2->offset[i] = offset;
        }
        if (index2->n < end + 1) index2->n = end + 1;
+       return (uint64_t)beg<<32 | end;
 }
 
 static void merge_chunks(ti_index_t *idx)
@@ -299,7 +300,7 @@ ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf)
        ti_index_t *idx;
        uint32_t last_bin, save_bin;
        int32_t last_coor, last_tid, save_tid;
-       uint64_t save_off, last_off, lineno = 0;
+       uint64_t save_off, last_off, lineno = 0, offset0 = (uint64_t)-1, tmp;
        kstring_t *str;
 
        str = calloc(1, sizeof(kstring_t));
@@ -322,13 +323,19 @@ ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf)
                }
                get_intv(idx, str, &intv);
                if (last_tid != intv.tid) { // change of chromosomes
+            if (last_tid>intv.tid )
+            {
+                fprintf(stderr,"[ti_index_core] the chromosome blocks not continuous at line %llu, is the file sorted?\n",(unsigned long long)lineno);
+                exit(1);
+            }
                        last_tid = intv.tid;
                        last_bin = 0xffffffffu;
                } else if (last_coor > intv.beg) {
                        fprintf(stderr, "[ti_index_core] the file out of order at line %llu\n", (unsigned long long)lineno);
                        exit(1);
                }
-               insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off);
+               tmp = insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off);
+               if (last_off == 0) offset0 = tmp;
                if (intv.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);
@@ -348,6 +355,10 @@ ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf)
        if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bgzf_tell(fp));
        merge_chunks(idx);
        fill_missing(idx);
+       if (offset0 != (uint64_t)-1 && idx->n && idx->index2[0].offset) {
+               int i, beg = offset0>>32, end = offset0&0xffffffffu;
+               for (i = beg; i <= end; ++i) idx->index2[0].offset[i] = 0;
+       }
 
        free(str->s); free(str);
        return idx;
@@ -645,8 +656,8 @@ ti_index_t *ti_index_load(const char *fn)
     char *fname = get_local_version(fn);
        if (fname == 0) return 0;
        idx = ti_index_load_local(fname);
+       if (idx == 0) fprintf(stderr, "[ti_index_load] fail to load the index: %s\n", fname);
     free(fname);
-       if (idx == 0) fprintf(stderr, "[ti_index_load] fail to load BAM index.\n");
        return idx;
 }
 
@@ -656,7 +667,7 @@ int ti_index_build2(const char *fn, const ti_conf_t *conf, const char *_fnidx)
        BGZF *fp, *fpidx;
        ti_index_t *idx;
        if ((fp = bgzf_open(fn, "r")) == 0) {
-               fprintf(stderr, "[ti_index_build2] fail to open the BAM file.\n");
+               fprintf(stderr, "[ti_index_build2] fail to open the file: %s\n", fn);
                return -1;
        }
        idx = ti_index_core(fp, conf);
@@ -803,6 +814,9 @@ ti_iter_t ti_iter_query(const ti_index_t *idx, int tid, int beg, int end)
                                if (p->list[j].v > min_off) off[n_off++] = p->list[j];
                }
        }
+       if (n_off == 0) {
+               free(bins); free(off); return iter;
+       }
        free(bins);
        {
                int l;