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Inti Pedroso  committed a863629

minor change

  • Participants
  • Parent commits 6ac60f5
  • Branches develop, feature/correction_gcv2 2
    1. feature/docs
    2. release/0.01

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Files changed (1)

File normalise_counts.py

 print time.ctime(), "Reading bam file"
 
 bam = pysam.Samfile(str(args.bam)) #('NA12878/NA12878.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.bam')
-ref_filename = bam.header['SQ'][0]['UR'].split('/')[-1]
+ref_filename = bam.header['SQ'][0]['UR'].split('/')[-1].split(' ')[0]
 
 
 if args.bed == 0: