Mercurial > repos > devteam > picard1106

comparison picard_wrapper.py @ 146:767bcb0a06df draft

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fixed downsamplesam
author Rayan Chikhi <chikhi@psu.edu>
date Mon, 21 Jul 2014 15:24:40 -0400
parents b2ca2d181fb4
children
comparison
equal deleted inserted replaced
143:b2ca2d181fb4 146:767bcb0a06df
802 haveTempout = True 802 haveTempout = True
803 803
804 elif pic.picname == "DownsampleSam": 804 elif pic.picname == "DownsampleSam":
805 cl.append('I=%s' % opts.input) 805 cl.append('I=%s' % opts.input)
806 output_string = opts.output 806 output_string = opts.output
807 if opts.datatype == 'sam': 807 if opts.output_format == 'sam':
808 output_string = output_string + ".sam" 808 output_string = output_string + ".sam"
809 cl.append('O=%s' % output_string) 809 cl.append('O=%s' % output_string)
810 if float(opts.probability) > 0: 810 if float(opts.probability) > 0:
811 cl.append('PROBABILITY=%s' % opts.probability) 811 cl.append('PROBABILITY=%s' % opts.probability)
812 if float(opts.seed) > 0: 812 if float(opts.seed) > 0:
813 cl.append('RANDOM_SEED=%s' % opts.seed) 813 cl.append('RANDOM_SEED=%s' % opts.seed)
814 stdouts,rval = pic.runPic(opts.jar, cl) 814 stdouts,rval = pic.runPic(opts.jar, cl)
815 if opts.input.endswith(".sam"): 815 if opts.output_format == 'sam':
816 renamed_output = output_string.replace(".sam", "") 816 os.rename(output_string, opts.output)
817 os.rename(output_string,renamed_output)
818 817
819 elif pic.picname == 'MeanQualityByCycle': 818 elif pic.picname == 'MeanQualityByCycle':
820 isPDF = 'MeanQualityByCycle.pdf' 819 isPDF = 'MeanQualityByCycle.pdf'
821 pdfpath = os.path.join(opts.outdir,isPDF) 820 pdfpath = os.path.join(opts.outdir,isPDF)
822 histpdf = isPDF 821 histpdf = isPDF