Merge pull request #49 from CenterForMedicalGeneticsGhent/v1.1.4

Automated paired-end processing

README.md

@@ -17,9 +17,8 @@ meant to be applicable not only to NIPT, but also gDNA, PGT, FFPE, LQB, ... etc.
 ## Mapping
 
 We found superior results through WisecondorX when using [bowtie2](https://github.com/BenLangmead/bowtie2) as a mapper. 
-I would recommend using the latest version of the human reference genome (GRCh38). Note that it is important that 
-**no** read quality filtering is executed prior the running WisecondorX: this software requires low-quality reads 
-to distinguish informative bins from non-informative ones.
+Note that it is important that **no** read quality filtering is executed prior to running WisecondorX: this software 
+requires low-quality reads to distinguish informative bins from non-informative ones.
 
 ## WisecondorX
 
@@ -67,7 +66,6 @@ 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)  
-`--paired` | Enables conversion for paired-end reads  
 
 
 &rarr; Bash recipe at `./pipeline/convert.sh`

setup.py

@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 from setuptools import setup, find_packages
 
-version = '1.1.3'
+version = '1.1.4'
 dl_version = 'master' if 'dev' in version else '{}'.format(version)
 
 setup(

wisecondorX/convert_tools.py

@@ -48,10 +48,9 @@ def convert_bam(args):
         if chr_name == 'Y':
             chr_name = '24'
 
-        if args.paired:
-
-            for read in bam_chr:
-                if not (read.is_proper_pair and read.is_read1):
+        for read in bam_chr:
+            if read.is_paired:
+                if not read.is_proper_pair:
                     reads_pairf += 1
                     continue
                 if larp == read.pos and larp2 == read.next_reference_start:
@@ -66,9 +65,7 @@ def convert_bam(args):
                 larp2 = read.next_reference_start
                 reads_seen += 1
                 larp = read.pos
-        else:
-
-            for read in bam_chr:
+            else:
                 if larp == read.pos:
                     reads_rmdup += 1
                 else:

wisecondorX/main.py

@@ -285,9 +285,6 @@ def main():
                                 type=float,
                                 default=5e3,
                                 help='Bin size (bp)')
-    parser_convert.add_argument('--paired',
-                                action='store_true',
-                                help='Use paired-end reads | default is single-end')
     parser_convert.set_defaults(func=tool_convert)
 
     parser_newref = subparsers.add_parser('newref',