debian/docs

-*manual.html
+assembler/*manual.html
 README.md

debian/patches/yaml_load.patch

@@ -14,3 +14,23 @@ Description: Specify yaml loader
          dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(cfg["dataset"].yaml_filename))
          support.pretty_print_reads(dataset_data, log)
  
+--- a/assembler/src/spades_pipeline/hammer_logic.py
++++ b/assembler/src/spades_pipeline/hammer_logic.py
+@@ -94,7 +94,7 @@ def prepare_config_ih(filename, cfg, ext
+     elif sys.version.startswith('3.'):
+         import pyyaml3 as pyyaml
+ 
+-    data = pyyaml.load(open(filename, 'r'))
++    data = pyyaml.load(open(filename, 'r'), Loader=pyyaml.FullLoader)
+     data["dataset"] = cfg.dataset_yaml_filename
+     data["working_dir"] = cfg.tmp_dir
+     data["output_dir"] = cfg.output_dir
+@@ -153,7 +153,7 @@ def run_hammer(corrected_dataset_yaml_fi
+         log.info("\n===== Skipping %s (already processed). \n" % "read error correction tool")
+         support.continue_from_here(log)
+ 
+-    corrected_dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'))
++    corrected_dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'), Loader=pyyaml.FullLoader)
+     remove_not_corrected_reads(cfg.output_dir)
+     is_changed = False
+     if cfg.gzip_output: