Fix hictk dump -t bins for files in .scool format

paulsengroup · Feb 11, 2024 · c76cbf9 · c76cbf9
1 parent 082348e
commit c76cbf9
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Showing 2 changed files with 20 additions and 4 deletions.
diff --git a/src/hictk/cli/cli_dump.cpp b/src/hictk/cli/cli_dump.cpp
@@ -224,6 +224,12 @@ void Cli::transform_args_dump_subcommand() {
     c.resolution = hic::utils::list_resolutions(c.uri).back();
   } else if (c.format == "mcool" && c.resolution == 0 && c.table == "chroms") {
     c.resolution = cooler::utils::list_resolutions(c.uri).back();
+  } else if (c.format == "scool" && (c.table == "chroms" || c.table == "bins")) {
+    const cooler::SingleCellFile sclr{c.uri};
+    if (sclr.cells().empty()) {
+      throw std::runtime_error("file does not contain any cell");
+    }
+    c.uri = fmt::format(FMT_STRING("{}::/cells/{}"), c.uri, *sclr.cells().begin());
   }
 
   if (_cli.get_subcommand("dump")->get_option("--range2")->empty()) {

diff --git a/test/scripts/hictk_dump_bins.sh b/test/scripts/hictk_dump_bins.sh
@@ -34,6 +34,9 @@ script_dir="$(readlink_py "$(dirname "$0")")"
 ref_cooler="$data_dir/integration_tests/4DNFIZ1ZVXC8.mcool"
 ref_hic="$data_dir/hic/4DNFIZ1ZVXC8.hic8"
 
+ref_scooler="$data_dir/cooler/single_cell_cooler_test_file.scool"
+cell_id='GSM2687248_41669_ACAGTG-R1-DpnII.100000.cool'
+
 export PATH="$PATH:$script_dir"
 
 if ! command -v cooler &> /dev/null; then
@@ -49,22 +52,29 @@ if [ $status -ne 0 ]; then
   exit $status
 fi
 
-if ! check_test_files_exist.sh "$ref_cooler"; then
+if ! check_test_files_exist.sh "$ref_cooler" "$ref_scooler" "$ref_hic"; then
   exit 1
 fi
 
 outdir="$(mktemp -d -t hictk-tmp-XXXXXXXXXX)"
 trap 'rm -rf -- "$outdir"' EXIT
 
-cooler dump -t bins "$ref_cooler::/resolutions/100000" | cut -f 1-3 > "$outdir/expected.chrom.sizes"
+cooler dump -t bins "$ref_cooler::/resolutions/100000" | cut -f 1-3 > "$outdir/expected1.chrom.sizes"
+cooler dump -t bins "$ref_scooler::/cells/$cell_id" | cut -f 1-3 > "$outdir/expected2.chrom.sizes"
+
 "$hictk_bin" dump -t bins "$ref_cooler::/resolutions/100000" > "$outdir/out.cooler.chrom.sizes"
 "$hictk_bin" dump -t bins --resolution 100000 "$ref_hic" > "$outdir/out.hic.chrom.sizes"
+"$hictk_bin" dump -t bins "$ref_scooler" > "$outdir/out.scooler.chrom.sizes"
+
+if ! compare_plain_files.sh "$outdir/expected1.chrom.sizes" "$outdir/out.cooler.chrom.sizes"; then
+  status=1
+fi
 
-if ! compare_plain_files.sh "$outdir/expected.chrom.sizes" "$outdir/out.cooler.chrom.sizes"; then
+if ! compare_plain_files.sh "$outdir/expected1.chrom.sizes" "$outdir/out.hic.chrom.sizes"; then
   status=1
 fi
 
-if ! compare_plain_files.sh "$outdir/expected.chrom.sizes" "$outdir/out.hic.chrom.sizes"; then
+if ! compare_plain_files.sh "$outdir/expected2.chrom.sizes" "$outdir/out.scooler.chrom.sizes"; then
   status=1
 fi