Set sensible defaults for one/zero based coords

paulsengroup · Dec 7, 2023 · 3c48ee3 · 3c48ee3
1 parent af0644c
commit 3c48ee3
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Showing 2 changed files with 11 additions and 4 deletions.
diff --git a/src/hictk/cli/cli_load.cpp b/src/hictk/cli/cli_load.cpp
@@ -76,7 +76,9 @@ void Cli::make_load_subcommand() {
   sc.add_flag(
       "--one-based,!--zero-based",
       c.one_based,
-      "Interpret genomic coordinates or bins as one/zero based.");
+      "Interpret genomic coordinates or bins as one/zero based.\n"
+      "By default coordinates are assumed to be one-based for interactions in\n"
+      "4dn and validapairs formats and zero-based otherwise.");
 
   sc.add_flag(
       "--count-as-float",
@@ -152,8 +154,15 @@ void Cli::validate_load_subcommand() const {
 
 void Cli::transform_args_load_subcommand() {
   auto& c = std::get<LoadConfig>(_config);
+  const auto& sc = *_cli.get_subcommand("load");
 
-  c.offset = c.one_based ? -1 : 0;
+  if (sc.get_option("--one-based")->empty()) {
+    if (c.format == "4dn" || c.format == "validpairs") {
+      c.offset = -1;
+    }
+  } else {
+    c.offset = c.one_based ? -1 : 0;
+  }
 
   // in spdlog, high numbers correspond to low log levels
   assert(c.verbosity > 0 && c.verbosity < 5);

diff --git a/test/scripts/hictk_load_coo.sh b/test/scripts/hictk_load_coo.sh
@@ -109,7 +109,6 @@ if [[ "$sorted" == true ]]; then
       --assume-sorted \
       --batch-size 1000000 \
       --bin-size 10000 \
-      --zero-based \
       "$outdir/chrom.sizes" \
       "$outdir/out.cool"
 else
@@ -120,7 +119,6 @@ else
       --assume-unsorted \
       --batch-size 1000000 \
       --bin-size 10000 \
-      --zero-based \
       "$outdir/chrom.sizes" \
       "$outdir/out.cool"
 fi