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from pysam.utils import PysamDispatcher
# samtools command line options to export in python
SAMTOOLS_DISPATCH = {
# samtools 'documented' commands
"view": ("view", None),
"head": ("head", None),
"sort": ("sort", None),
"mpileup": ("mpileup", None),
"consensus": ("consensus", None),
"depth": ("depth", None),
"faidx": ("faidx", None),
"fqidx": ("fqidx", None),
"tview": ("tview", None),
"index": ("index", None),
"idxstats": ("idxstats", None),
"fixmate": ("fixmate", None),
"flagstat": ("flagstat", None),
"calmd": ("calmd", None),
"merge": ("merge", None),
"markdup": ("markdup", None),
"rmdup": ("rmdup", None),
"reference": ("reference", None),
"reheader": ("reheader", None),
"cat": ("cat", None),
"targetcut": ("targetcut", None),
"phase": ("phase", None),
"bam2fq": ("bam2fq", None),
"dict": ("dict", None),
"addreplacerg": ("addreplacerg", None),
"pad2unpad": ("pad2unpad", None),
"depad": ("pad2unpad", None),
"bedcov": ("bedcov", None),
"coverage": ("coverage", None),
"bamshuf": ("bamshuf", None),
"collate": ("collate", None),
"stats": ("stats", None),
"fasta": ("fasta", None),
"fastq": ("fastq", None),
"quickcheck": ("quickcheck", None),
"split": ("split", None),
"flags": ("flags", None),
"ampliconclip": ("ampliconclip", None),
"ampliconstats": ("ampliconstats", None),
"version": ("version", None),
"fqimport": ("import", None),
"samples": ("samples", None),
}
# instantiate samtools commands as python functions
for key, options in SAMTOOLS_DISPATCH.items():
cmd, parser = options
globals()[key] = PysamDispatcher("samtools", cmd, parser)
__all__ = list(SAMTOOLS_DISPATCH)
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