Added --normdup flag

README.md

@@ -31,7 +31,8 @@ downloaded, however, it does not install R [dependencies](#dependencies).
 pip install -U git+https://github.com/CenterForMedicalGeneticsGhent/WisecondorX
 ```
 
-Alternatively, [Conda](https://conda.io/docs/) additionally installs all necessary [depedencies](#dependencies), however, the latest version might not be downloaded.
+Alternatively, [Conda](https://conda.io/docs/) additionally installs all necessary [depedencies](#dependencies), 
+however, the latest version might not be downloaded.
 ```bash
 
 conda install -f -c conda-forge -c bioconda wisecondorx
@@ -65,6 +66,7 @@ WisecondorX convert input.bam output.npz [--optional arguments]
 <br>Optional argument <br><br> | Function  
 :--- | :---  
 `--binsize x` | Size per bin in bp; the reference bin size should be a multiple of this value. Note that this parameter does not impact the resolution, yet it can be used to optimize processing speed (default: x=5e3)  
+`--normdup` | Use this flag to avoid duplicate removal  
 
 
 &rarr; Bash recipe at `./pipeline/convert.sh`

setup.py

@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 from setuptools import setup, find_packages
 
-version = '1.1.4'
+version = '1.1.5'
 dl_version = 'master' if 'dev' in version else '{}'.format(version)
 
 setup(

wisecondorX/convert_tools.py

@@ -53,7 +53,7 @@ def convert_bam(args):
                 if not read.is_proper_pair:
                     reads_pairf += 1
                     continue
-                if larp == read.pos and larp2 == read.next_reference_start:
+                if not args.normdup and larp == read.pos and larp2 == read.next_reference_start:
                     reads_rmdup += 1
                 else:
                     if read.mapping_quality >= 1:
@@ -66,7 +66,7 @@ def convert_bam(args):
                 reads_seen += 1
                 larp = read.pos
             else:
-                if larp == read.pos:
+                if not args.normdup and larp == read.pos:
                     reads_rmdup += 1
                 else:
                     if read.mapping_quality >= 1:

wisecondorX/main.py

@@ -285,6 +285,9 @@ def main():
                                 type=float,
                                 default=5e3,
                                 help='Bin size (bp)')
+    parser_convert.add_argument('--normdup',
+                                action='store_true',
+                                help='Do not remove duplicates')
     parser_convert.set_defaults(func=tool_convert)
 
     parser_newref = subparsers.add_parser('newref',