Merge pull request #8 from a-slide/dev

Dev

pycoMeth/__init__.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
 
 # Define self package variable
-__version__ = "0.2.7"
+__version__ = "0.2.8"
 __description__ = 'Python package for nanopore DNA methylation analysis downstream to Nanopolish'

pycoMeth/__main__.py

@@ -61,8 +61,8 @@ def main(args=None):
     sp_met_io = sp_met.add_argument_group("Input/Output options")
     arg_from_docstr(sp_met_io, f, "aggregate_fn_list", "i")
     arg_from_docstr(sp_met_io, f, "ref_fasta_fn", "f")
-    arg_from_docstr(sp_met_io, f, "output_tsv_fn", "b")
-    arg_from_docstr(sp_met_io, f, "output_bed_fn", "t")
+    arg_from_docstr(sp_met_io, f, "output_bed_fn", "b")
+    arg_from_docstr(sp_met_io, f, "output_tsv_fn", "t")
     sp_met_ms = sp_met.add_argument_group("Misc options")
     arg_from_docstr(sp_met_ms, f, "max_missing", "m")
     arg_from_docstr(sp_met_ms, f, "min_diff_llr", "l")
@@ -76,8 +76,8 @@ def main(args=None):
     sp_cgi.set_defaults(func=f)
     sp_cgi_io = sp_cgi.add_argument_group("Input/Output options")
     arg_from_docstr(sp_cgi_io, f, "ref_fasta_fn", "f")
-    arg_from_docstr(sp_cgi_io, f, "output_tsv_fn", "b")
-    arg_from_docstr(sp_cgi_io, f, "output_bed_fn", "t")
+    arg_from_docstr(sp_cgi_io, f, "output_bed_fn", "b")
+    arg_from_docstr(sp_cgi_io, f, "output_tsv_fn", "t")
     sp_cgi_ms = sp_cgi.add_argument_group("Misc options")
     arg_from_docstr(sp_cgi_ms, f, "merge_gap", "m")
     arg_from_docstr(sp_cgi_ms, f, "min_win_len", "w")

setup.py

@@ -5,7 +5,7 @@
 
 # Define package info
 name = "pycoMeth"
-version = "0.2.7"
+version = "0.2.8"
 description = 'Python package for nanopore DNA methylation analysis downstream to Nanopolish'
 with open("README.md", "r") as fh:
     long_description = fh.read()