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src/b/i/biopython-HEAD/Tests/test_samtools_tool.py   biopython(Download)
from Bio.Sequencing.Applications import SamtoolsIdxstatsCommandline
from Bio.Sequencing.Applications import SamtoolsIndexCommandline
from Bio.Sequencing.Applications import SamtoolsMergeCommandline
from Bio.Sequencing.Applications import SamtoolsMpileupCommandline
from Bio.Sequencing.Applications import SamtoolsSortCommandline
    def test_merge(self):
        cmdline = SamtoolsMergeCommandline(samtools_exe)
        cmdline.set_parameter("input_bam", [self.bamfile1, self.bamfile2])
        cmdline.set_parameter("out_bam", self.outbamfile)
        cmdline.set_parameter("f", True)  # Overwrite out.bam if it exists
        stdout, stderr = cmdline()