Change default compression level of .hic files from 9 to 10

docs/cli_reference.rst

@@ -115,7 +115,7 @@ hictk convert
                                 When converting from hic to cool, only two threads will be used.
     -l,--compression-lvl UINT:INT in [1 - 12] [6]
                                 Compression level used to compress interactions.
-                                Defaults to 6 and 9 for .cool and .hic files, respectively.
+                                Defaults to 6 and 10 for .cool and .hic files, respectively.
     -f,--force                  Overwrite existing files (if any).
 
 hictk dump
@@ -215,7 +215,7 @@ hictk load
                                 Number of pixels to buffer in memory.
     -l,--compression-lvl UINT:INT bounded to [1 - 12]
                                 Compression level used to compress interactions.
-                                Defaults to 6 and 9 for .cool and .hic files, respectively.
+                                Defaults to 6 and 10 for .cool and .hic files, respectively.
     -t,--threads UINT:UINT in [1 - 16] [1]
                                 Maximum number of parallel threads to spawn.
                                 When loading interactions in a .cool file, only a single thread will be used.
@@ -244,7 +244,7 @@ hictk merge
                                 Number of pixels to store in memory before writing to disk.
     -l,--compression-lvl UINT:INT bounded to [1 - 12]
                                 Compression level used to compress interactions.
-                                Defaults to 6 and 9 for .cool and .hic files, respectively.
+                                Defaults to 6 and 10 for .cool and .hic files, respectively.
     -t,--threads UINT:UINT in [1 - 16] [1]
                                 Maximum number of parallel threads to spawn.
                                 When merging interactions in Cooler format, only a single thread will be used.

src/hictk/cli/cli_convert.cpp

@@ -111,7 +111,7 @@ void Cli::make_convert_subcommand() {
       "-l,--compression-lvl",
       c.compression_lvl,
       "Compression level used to compress interactions.\n"
-      "Defaults to 6 and 9 for .cool and .hic files, respectively.")
+      "Defaults to 6 and 10 for .cool and .hic files, respectively.")
       ->check(CLI::Range(1, 12))
       ->capture_default_str();
   sc.add_flag(
@@ -243,7 +243,7 @@ void Cli::transform_args_convert_subcommand() {
   c.tmp_dir /= c.path_to_output.filename().string() + ".tmp";
 
   if (sc.get_option("--compression-lvl")->empty()) {
-    c.compression_lvl = c.output_format == "hic" ? 9 : 6;
+    c.compression_lvl = c.output_format == "hic" ? 10 : 6;
   }
 }
 

src/hictk/cli/cli_load.cpp

@@ -109,7 +109,7 @@ void Cli::make_load_subcommand() {
       "-l,--compression-lvl",
       c.compression_lvl,
       "Compression level used to compress interactions.\n"
-      "Defaults to 6 and 9 for .cool and .hic files, respectively.")
+      "Defaults to 6 and 10 for .cool and .hic files, respectively.")
       ->check(CLI::Bound(1, 12));
 
   sc.add_option(
@@ -201,7 +201,7 @@ void Cli::transform_args_load_subcommand() {
   c.tmp_dir /= (std::filesystem::path(c.output_path).filename().string() + ".tmp");
 
   if (sc.get_option("--compression-lvl")->empty()) {
-    c.compression_lvl = c.output_format == "hic" ? 9 : 6;
+    c.compression_lvl = c.output_format == "hic" ? 10 : 6;
   }
 
   // in spdlog, high numbers correspond to low log levels

src/hictk/cli/cli_merge.cpp

@@ -71,7 +71,7 @@ void Cli::make_merge_subcommand() {
       "-l,--compression-lvl",
       c.compression_lvl,
       "Compression level used to compress interactions.\n"
-      "Defaults to 6 and 9 for .cool and .hic files, respectively.")
+      "Defaults to 6 and 10 for .cool and .hic files, respectively.")
       ->check(CLI::Bound(1, 12));
 
   sc.add_option(
@@ -181,7 +181,7 @@ void Cli::transform_args_merge_subcommand() {
   c.output_format = c.output_file.empty() ? "text" : infer_output_format(c.output_file);
 
   if (sc.get_option("--compression-lvl")->empty()) {
-    c.compression_lvl = c.output_format == "hic" ? 9 : 6;
+    c.compression_lvl = c.output_format == "hic" ? 10 : 6;
   }
 
   c.tmp_dir /= c.output_file.filename().string() + ".tmp";

src/hictk/cli/cli_zoomify.cpp

@@ -286,7 +286,7 @@ void Cli::transform_args_zoomify_subcommand() {
   }
 
   if (sc.get_option("--compression-lvl")->empty()) {
-    c.compression_lvl = c.output_format == "hic" ? 9 : 6;
+    c.compression_lvl = c.output_format == "hic" ? 10 : 6;
   }
 
   c.tmp_dir /= c.path_to_output.filename().string() + ".tmp";