added missing arguments and bumped version

Author: gtonkinhill

panaroo/__init__.py

@@ -1,2 +1,2 @@
 '''An updated pipeline for pangenome investigation'''
-__version__ = '1.5.3'
+__version__ = '1.6.0'

panaroo/generate_qc_plots.py

@@ -346,7 +346,7 @@ def plot_mash_contam(mash_contam_file, outdir):
     return
 
 
-def generate_qc_plot(method, input_files, outdir, n_cpu, ref_db=None, no_plot=False):
+def generate_qc_plot(method, input_files, outdir, n_cpu, ref_db=None, no_plot=False, random_seed=1):
 
     # plot MDS
     if method in ["mds", "all"]:

panaroo/integrate.py

@@ -101,6 +101,11 @@ def get_options(
         type=float,
         default=0.1)
 
+    matching.add_argument("--family_len_dif_percent",
+                          dest="family_len_dif_percent",
+                          help="length difference cutoff at the gene family level (default=0.0)",
+                          type=float)
+
     parser.add_argument(
         "--min_edge_support_sv",
         dest="min_edge_support_sv",
@@ -301,6 +306,7 @@ def main():
                  len_dif_percent=args.len_dif_percent,
                  pid=args.id,
                  family_threshold=args.family_threshold,
+                 family_len_dif_percent=args.family_len_dif_percent,
                  length_outlier_support_proportion=args.
                  length_outlier_support_proportion,
                  merge_para=args.merge_paralogs,

panaroo/merge_graphs.py

@@ -256,6 +256,7 @@ def merge_graphs(directories,
                  len_dif_percent,
                  pid,
                  family_threshold,
+                 family_len_dif_percent,
                  length_outlier_support_proportion,
                  merge_para,
                  output_dir,