change contig alias

TileDB-Inc · Dec 8, 2023 · c48d6ed · c48d6ed
1 parent 5ae4b64
commit c48d6ed
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/apis/python/tests/test_tiledbvcf.py b/apis/python/tests/test_tiledbvcf.py
@@ -1588,7 +1588,7 @@ def test_bed_array(tmp_path, test_ds_v4):
 
  # Add aliases to the array metadata
  with tiledb.Array(bed_array, "w") as A:
- A.meta["alias chrom"] = "chrom"
+ A.meta["alias contig"] = "chrom"
  A.meta["alias start"] = "chromStart"
  A.meta["alias end"] = "chromEnd"
 

diff --git a/libtiledbvcf/src/vcf/region.cc b/libtiledbvcf/src/vcf/region.cc
@@ -142,15 +142,15 @@ void Region::read_bed_array(
  std::shared_ptr<Array> bed_array, std::list<Region>& result) {
  // Define the metadata keys for the BED array which contain the aliases
  // for the column names
- static const std::string CHROM = "alias chrom";
+ static const std::string CONTIG = "alias contig";
  static const std::string START = "alias start";
  static const std::string END = "alias end";
 
  // Read the column name aliases from the array metadata
  std::map<std::string, std::string> column_alias;
  std::vector<std::string> column_names;
 
- for (const auto& key : {CHROM, START, END}) {
+ for (const auto& key : {CONTIG, START, END}) {
  const void* value = nullptr;
  tiledb_datatype_t value_type;
  uint32_t value_num = 0;
@@ -177,7 +177,7 @@ void Region::read_bed_array(
  auto num_rows = mq.results()->num_rows();
 
  for (unsigned int i = 0; i < num_rows; i++) {
- auto chrom = std::string(mq.string_view(column_alias[CHROM], i));
+ auto chrom = std::string(mq.string_view(column_alias[CONTIG], i));
  auto chromStart = mq.data<uint64_t>(column_alias[START])[i];
  auto chromEnd = mq.data<uint64_t>(column_alias[END])[i];