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src/b/i/biopython-HEAD/Tests/test_samtools_tool.py   biopython(Download)
from Bio.Sequencing.Applications import SamtoolsMergeCommandline
from Bio.Sequencing.Applications import SamtoolsMpileupCommandline
from Bio.Sequencing.Applications import SamtoolsSortCommandline
#TODO from Bio.Sequencing.Applications import SamtoolsPhaseCommandline
#TODO from Bio.Sequencing.Applications import SamtoolsReheaderCommandline
    def test_sort(self):
        cmdline = SamtoolsSortCommandline(samtools_exe)
        cmdline.set_parameter("input_bam", self.bamfile1)
        cmdline.set_parameter("out_prefix", "SamBam/out")
        stdout, stderr = cmdline()