wrapper for running in parallel
(args)
| 214 | return gender |
| 215 | |
| 216 | def preprocessWrapper(args): |
| 217 | """ wrapper for running in parallel """ |
| 218 | |
| 219 | starttime = time.time() |
| 220 | logging.info("Preprocessing %s" % args.input) |
| 221 | |
| 222 | if args.pass_only: |
| 223 | filtering = "*" |
| 224 | else: |
| 225 | filtering = args.filters_only |
| 226 | |
| 227 | if args.bcf and not args.output.endswith(".bcf"): |
| 228 | args.output += ".bcf" |
| 229 | |
| 230 | preprocess(args.input, |
| 231 | args.output, |
| 232 | args.ref, |
| 233 | args.locations, |
| 234 | filtering, |
| 235 | args.fixchr, |
| 236 | args.regions_bedfile, |
| 237 | args.targets_bedfile, |
| 238 | args.preprocessing_leftshift, |
| 239 | args.preprocessing_decompose, |
| 240 | args.preprocessing_norm, |
| 241 | args.window, |
| 242 | args.threads, |
| 243 | args.gender, |
| 244 | args.somatic_allele_conversion, |
| 245 | convert_gvcf_to_vcf=args.convert_gvcf_to_vcf) |
| 246 | |
| 247 | elapsed = time.time() - starttime |
| 248 | logging.info("preprocess for %s -- time taken %.2f" % (args.input, elapsed)) |
| 249 | |
| 250 | |
| 251 | def updateArgs(parser): |