radpipe/stages.py
def filter_bam(self, input, output, extra_options):
        '''Filter BAM file with Samtools view'''
        command = "samtools view -b {extra_options} {input} > {output} && " \
                  "samtools index {output}".format(extra_options=extra_options,
                          input=input, output=output)
        run_stage(self.state, "filter_bam", command)
Filter BAM file with Samtools view
Filter BAM file with Samtools view
Filter BAM file with Samtools view
def filter_bam(self, input, output, extra_options):
        command = "samtools view -b {extra_options} {input} > {output} && " \
                  "samtools index {output}".format(extra_options=extra_options,
                          input=input, output=output)
        run_stage(self.state, "filter_bam", command)
def filter_bam ( self , input , output , extra_options ) : command = "samtools view -b {extra_options} {input} > {output} && " "samtools index {output}" . format ( extra_options = extra_options , input = input , output = output ) run_stage ( self . state , "filter_bam" , command )
Filter BAM file with Samtools view
Filter BAM file with Samtools view
'''Filter BAM file with Samtools view'''
self
input
output
extra_options