add VCF.load_index to allow explicitly loading an index

Author: brentp

src/hts/private/hts_concat.h

@@ -235,6 +235,7 @@ void hts_idx_finish(hts_idx_t *idx, uint64_t final_offset);
 
 void hts_idx_save(const hts_idx_t *idx, const char *fn, int fmt);
 hts_idx_t *hts_idx_load(const char *fn, int fmt);
+hts_idx_t *hts_idx_load2(const char *fn, const char *fnidx);
 
 
 uint8_t *hts_idx_get_meta(hts_idx_t *idx, int *l_meta);

src/hts/private/hts_concat.nim

@@ -294,6 +294,8 @@ proc hts_idx_save*(idx: ptr hts_idx_t; fn: cstring; fmt: cint) {.cdecl,
     importc: "hts_idx_save", dynlib: libname.}
 proc hts_idx_load*(fn: cstring; fmt: cint): ptr hts_idx_t {.cdecl,
     importc: "hts_idx_load", dynlib: libname.}
+proc hts_idx_load2*(fn: cstring; fnidx: cstring): ptr hts_idx_t {.cdecl,
+    importc: "hts_idx_load2", dynlib: libname.}
 proc hts_idx_get_meta*(idx: ptr hts_idx_t; l_meta: ptr cint): ptr uint8 {.cdecl,
     importc: "hts_idx_get_meta", dynlib: libname.}
 proc hts_idx_set_meta*(idx: ptr hts_idx_t; l_meta: uint32; meta: ptr uint8; is_copy: cint): cint {.
@@ -637,7 +639,7 @@ const
 ##
 
 type
-  INNER_C_UNION_hts_concat_544* {.bycopy.} = object {.union.}
+  INNER_C_UNION_hts_concat_545* {.bycopy.} = object {.union.}
     i*: int32                  ##  integer value
     f*: cfloat                 ##  float value
 
@@ -667,7 +669,7 @@ type
     key*: cint                 ##  key: numeric tag id, the corresponding string is bcf_hdr_t::id[BCF_DT_ID][$key].key
     `type`*: cint
     len*: cint                 ##  type: one of BCF_BT_* types; len: vector length, 1 for scalars
-    v1*: INNER_C_UNION_hts_concat_544 ##  only set if $len==1; for easier access
+    v1*: INNER_C_UNION_hts_concat_545 ##  only set if $len==1; for easier access
     vptr*: ptr uint8            ##  pointer to data array in bcf1_t->shared.s, excluding the size+type and tag id bytes
     vptr_len*: uint32          ##  length of the vptr block or, when set, of the vptr_mod block, excluding offset
     vptr_off* {.bitsize: 31.}: uint32 ##  vptr offset, i.e., the size of the INFO key plus size+type bytes

src/hts/vcf.nim

@@ -527,6 +527,14 @@ iterator items*(v:VCF): Variant =
     stderr.write_line "last read variant:", variant.tostring()
     quit(2)
 
+proc load_index*(v: VCF, path: string) =
+  ## load the index at the given path (remote or local).
+  v.bidx = hts_idx_load2(v.fname, path)
+  if v.bidx == nil:
+    v.tidx = tbx_index_load2(v.fname, path)
+  if v.bidx == nil and v.tidx == nil:
+    raise newException(OSError, "unable to load index at:" & path)
+
 iterator vquery(v:VCF, region:string): Variant =
   ## internal iterator for VCF regions called from query()
   if v.tidx == nil:

tests/other-for-test.bcf.csi

@@ -228,6 +228,10 @@ suite "vcf suite":
       check variant.info.set("myflag", val) == Status.OK
       check "myflag" notin variant.tostring()
 
+  test "load index":
+    var vcf:VCF
+    check open(vcf, "tests/test.bcf")
+    vcf.load_index("tests/other-for-test.bcf.csi")
 
   test "remove info from header":
     var vcf:VCF