Switch back to using multiple threads for CRAM generation in benchmark mode, as even with a single thread the file sizes can differ

Author: heathsc

gemBS/__init__.py

@@ -799,9 +799,9 @@ def mapping(name=None,index=None,fliInfo=None,inputFiles=None,ftype=None,filetyp
     if benchmark_mode:
         bamSort.append("--no-PG")
     if outfile.endswith('.cram'):
-        bamSort.extend(['-O', 'CRAM']);
+        bamSort.extend(['-O', 'CRAM', "-@", sort_threads]);
         if not benchmark_mode:
-            bamSort.extend(['--reference', greference, "-@", sort_threads]);
+            bamSort.extend(['--reference', greference]);
     else:
         bamSort.extend(["-@", sort_threads]);
 
@@ -847,9 +847,9 @@ def merging(inputs=None,sample=None,threads="1",outname=None,tmpDir="/tmp/",benc
         if benchmark_mode:
             bammerging.append("--no-PG")
         if bam_filename.endswith('.cram'):
-            bammerging.extend(['-O', 'CRAM']);
+            bammerging.extend(['-O', 'CRAM', '--threads', threads]);
             if not benchmark_mode:
-                bammerging.extend(['--reference', greference, '--threads', threads]);
+                bammerging.extend(['--reference', greference]);
         else:
             bammerging.extend(['--threads', threads]);
 

gemBS/production.py

@@ -989,7 +989,7 @@ def run(self,args):
             if len(self.contig_list) == 1:
                 if os.path.isfile(self.contig_list[0]):
                     #Check if contig_list is a file or just a list of chromosomes
-                    #Parse file to extract chromosme list 
+                    #Parse file to extract chromosome list 
                     tmp_list = []
                     with open(self.contig_list[0] , 'r') as chromFile:
                         for line in chromFile:
@@ -1360,7 +1360,7 @@ def register(self,parser):
         parser.add_argument('-N','--non-cpg', dest="non_cpg", action="store_true", help="Output gemBS bed with non-cpg sites.")
         parser.add_argument('-B','--bed-methyl', dest="bedMethyl", action="store_true", help="Output bedMethyl files (bed and bigBed)")
         parser.add_argument('-S','--snps', dest="snps", action="store_true",help="Output SNPs")
-        parser.add_argument('--extract-threads', dest="extract_threads", metavar="THREADS", help='Number of extra threads for extract step')
+        parser.add_argument('-t','--extract-threads', dest="extract_threads", metavar="THREADS", help='Number of extra threads for extract step')
         parser.add_argument('--snp-list', dest="snp_list", help="List of SNPs to output")
         parser.add_argument('--snp-db', dest="snp_db", help="dbSNP_idx processed SNP idx")
         parser.add_argument('--dry-run', dest="dry_run", action="store_true", help="Output mapping commands without execution")