Merge pull request #76 from CenterForMedicalGeneticsGhent/bug/cram_su…

…pport Bug/cram support
CenterForMedicalGeneticsGhent · Mar 31, 2021 · c1d8057 · c1d8057
2 parents 5c9f1f1 + b520919
commit c1d8057
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Showing 4 changed files with 13 additions and 5 deletions.
diff --git a/README.md b/README.md
@@ -65,6 +65,7 @@ WisecondorX convert input.sam/bam/cram output.npz [--optional arguments]
 
 <br>Optional argument <br><br> | Function  
 :--- | :---  
+`--reference x` | Fasta reference to be used with cram inputs
 `--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  
 

diff --git a/setup.py b/setup.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 from setuptools import setup, find_packages
 
-version = '1.2.2'
+version = '1.2.3'
 dl_version = 'master' if 'dev' in version else '{}'.format(version)
 
 setup(

diff --git a/wisecondorX/convert_tools.py b/wisecondorX/convert_tools.py
@@ -24,7 +24,11 @@ def convert_reads(args):
     elif args.infile.endswith(".bam"):
         reads_file = pysam.AlignmentFile(args.infile, 'rb')
     elif args.infile.endswith(".cram"):
-        reads_file = pysam.AlignmentFile(args.infile, 'rc')
+        if args.reference is not None:
+            reads_file = pysam.AlignmentFile(args.infile, 'rc', reference_filename=args.reference)
+        else:
+            logging.error("Cram support requires a reference file, please use the --reference argument")
+            sys.exit(1)
     else:
         logging.error(
             "Unsupported input file type. Make sure your input filename has a correct extension (sam/bam/cram)")

diff --git a/wisecondorX/main.py b/wisecondorX/main.py
@@ -264,22 +264,25 @@ def output_gender(args):
 def main():
     warnings.filterwarnings('ignore')
 
-    parser = argparse.ArgumentParser(description='wisecondorX')
+    parser = argparse.ArgumentParser(description='WisecondorX')
     parser.add_argument('--loglevel',
                         type=str,
                         default='INFO',
                         choices=['info', 'warning', 'debug', 'error', 'critical'])
     subparsers = parser.add_subparsers()
 
     parser_convert = subparsers.add_parser('convert',
-                                           description='Convert and filter a .bam file to a .npz',
+                                           description='Convert and filter a aligned reads to .npz',
                                            formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser_convert.add_argument('infile',
                                 type=str,
-                                help='.bam input file for conversion')
+                                help='aligned reads input for conversion')
     parser_convert.add_argument('outfile',
                                 type=str,
                                 help='Output .npz file')
+    parser_convert.add_argument('-r', '--reference',
+                                type=str,
+                                help='Fasta reference to be used during cram conversion')
     parser_convert.add_argument('--binsize',
                                 type=float,
                                 default=5e3,