comparison picard_wrapper.py @ 143:b2ca2d181fb4 draft

fixed downsample sam in picard1106 (accept bam)

142:844fa42ad305

    elif pic.picname == 'SamFormatConverter':
        cl.append('INPUT=%s' % opts.input)
        cl.append('OUTPUT=%s' % tempout)
        pic.runPic(opts.jar, cl)
        haveTempout = True
    elif pic.picname == "DownsampleSam":
        cl.append('I=%s' % opts.input)
        mystring = opts.output
        mystringsam = mystring + ".sam"
        cl.append('O=%s' % mystringsam)
        if float(opts.probability) > 0:
            cl.append('PROBABILITY=%s' % opts.probability)
        if float(opts.seed) > 0:
            cl.append('RANDOM_SEED=%s' % opts.seed)
        stdouts,rval = pic.runPic(opts.jar, cl)
        myoutput = mystringsam.replace(".sam", "")
        os.rename(mystringsam,myoutput)

    elif pic.picname == 'MeanQualityByCycle':
        isPDF = 'MeanQualityByCycle.pdf'
        pdfpath = os.path.join(opts.outdir,isPDF)
        histpdf = isPDF

143:b2ca2d181fb4

    elif pic.picname == 'SamFormatConverter':
        cl.append('INPUT=%s' % opts.input)
        cl.append('OUTPUT=%s' % tempout)
        pic.runPic(opts.jar, cl)
        haveTempout = True

    elif pic.picname == "DownsampleSam":
        cl.append('I=%s' % opts.input)
        output_string = opts.output
        if opts.datatype == 'sam':
            output_string = output_string + ".sam"
        cl.append('O=%s' % output_string)
        if float(opts.probability) > 0:
            cl.append('PROBABILITY=%s' % opts.probability)
        if float(opts.seed) > 0:
            cl.append('RANDOM_SEED=%s' % opts.seed)
        stdouts,rval = pic.runPic(opts.jar, cl)
        if opts.input.endswith(".sam"):
            renamed_output = output_string.replace(".sam", "")
            os.rename(output_string,renamed_output)

    elif pic.picname == 'MeanQualityByCycle':
        isPDF = 'MeanQualityByCycle.pdf'
        pdfpath = os.path.join(opts.outdir,isPDF)
        histpdf = isPDF