Merge pull request #143 from TileDB-Inc/aw/ch2921/add-null-attr-array

Add array and cli/py tests for querying records with null attributes
TileDB-Inc · Aug 12, 2020 · 44f2891 · 44f2891
2 parents 4e311a6 + 8a3bee4
commit 44f2891
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Showing 2 changed files with 17 additions and 2 deletions.
diff --git a/apis/python/tests/test_tiledbvcf.py b/apis/python/tests/test_tiledbvcf.py
@@ -352,7 +352,7 @@ def test_read_null_attrs(tmp_path):
 
     ds = tiledbvcf.Dataset(uri, mode='r')
     df = ds.read(attrs=['sample_name', 'pos_start', 'pos_end',
-                        'info_BaseQRankSum', 'info_DP', 'fmt_DP'],
+                        'info_BaseQRankSum', 'info_DP', 'fmt_DP', 'fmt_MIN_DP'],
                  regions=['1:12700-13400', '1:69500-69800'])
     expected_df = pd.DataFrame(
         {'sample_name': pd.Series(
@@ -372,7 +372,9 @@ def test_read_null_attrs(tmp_path):
                                   np.array([89], dtype=np.int32), None,
                                   np.array([24], dtype=np.int32), None, None]),
             'fmt_DP': pd.Series([0, 0, 15, 64, 6, 2, 180,
-                                     88, 97, 24, 23, 21], dtype=np.int32)})
+                                     88, 97, 24, 23, 21], dtype=np.int32),
+            'fmt_MIN_DP': pd.Series([0, 0, 14, 30, 3, 1, 20,
+                                     None, 24, None, 23, 19])})
     _check_dfs(expected_df, df)
 
 

diff --git a/libtiledbvcf/test/run-cli-tests.sh b/libtiledbvcf/test/run-cli-tests.sh
@@ -21,6 +21,7 @@ function clean_up {
            ingested_from_file ingested_diff_order ingested_buffered \
            ingested_sep_indexes ingested_dupe_end_pos \
            ingested_dupe_start_pos errored_dupe_start_pos \
+           ingested_null_attr \
            ingested_capacity HG01762.vcf HG00280.vcf tmp.bed tmp1.vcf tmp2.vcf \
            region-map.txt pfx.tsv
     rm -rf "$upload_dir"
@@ -285,6 +286,18 @@ EOF
 rm -f /tmp/pfx.tsv
 rm -f HG00280.vcf HG01762.vcf region-map.txt $upload_dir/*
 
+echo "Export records with a null fmt attribute (#142)"
+create_register_ingest ingested_null_attr ${input_dir}/small3.bcf ${input_dir}/small.bcf
+$tilevcf export -u ingested_null_attr -Ot -tPOS,S:MIN_DP -r1:69511-69512 -v -o pfx.tsv -d /tmp/ || exit 1
+diff -wq /tmp/pfx.tsv <(
+cat <<EOF
+SAMPLE	POS	S:MIN_DP
+HG00280	69511	.
+HG00280	69512	24
+EOF
+) || exit 1
+rm -f /tmp/pfx.tsv
+
 echo "Export non-contiguous samples (#79)"
 $tilevcf export -u ingested_3_samples -Ob -v -s G1,G3 || exit 1
 rm -f G{1,3}.bcf