Merge pull request #26 from B-UMMI/dev

Update master to version 4.1.0

ReMatCh/__init__.py

@@ -1 +1 @@
-__version__ = '4.0.1'
+__version__ = '4.1.0'

ReMatCh/modules/rematch_module.py

@@ -3,10 +3,10 @@
 import functools
 import sys
 import pickle
-from . import utils
 
 # https://chrisyeh96.github.io/2017/08/08/definitive-guide-python-imports.html#case-2-syspath-could-change
 sys.path.insert(0, os.path.dirname(os.path.realpath(__file__)))
+import utils
 
 
 def index_fasta_samtools(fasta, region_none, region_outfile_none, print_comand_true):
@@ -974,9 +974,14 @@ def analyse_sequence_data(bam_file, sequence_information, outdir, counter, refer
                                                  minimum_depth_frequency_dominant_allele,
                                                  sequence_information['sequence'], length_extra_seq)
 
-            count_absent, percentage_low_coverage, mean_coverage = \
-                get_coverage_report(coverage, sequence_information['length'], minimum_depth_presence,
-                                    minimum_depth_call, length_extra_seq)
+            try:
+                count_absent, percentage_low_coverage, mean_coverage = \
+                    get_coverage_report(coverage, sequence_information['length'], minimum_depth_presence,
+                                        minimum_depth_call, length_extra_seq)
+            except KeyError:
+                print('ERROR: KeyError')
+                print(sequence_information)
+                raise KeyError
 
     utils.save_variable_to_pickle([run_successfully, counter, number_multi_alleles, count_absent,
                                    percentage_low_coverage, mean_coverage, consensus_sequence, number_diferences],

ReMatCh/rematch.py

@@ -9,7 +9,7 @@
 
 Copyright (C) 2019 Miguel Machado <[email protected]>
 
-Last modified: January 02, 2019
+Last modified: August 08, 2019
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by