/usr/lib/python3/dist-packages/ngs/Pileup.py is in python3-ngs 1.3.0-3.
This file is owned by root:root, with mode 0o644.
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#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
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# thus cannot be copyrighted. This software/database is freely available
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from ctypes import c_void_p, c_char, c_uint32, c_int64
from . import NGS
from .String import getNGSString, getNGSValue
from .PileupEventIterator import PileupEventIterator
# Represents a slice through a stack of Alignments at a given position on the Reference
class Pileup(PileupEventIterator):
# ----------------------------------------------------------------------
# Reference
def getReferenceSpec(self):
return getNGSString(self, NGS.lib_manager.PY_NGS_PileupGetReferenceSpec)
def getReferencePosition(self):
return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupGetReferencePosition, c_int64)
def getReferenceBase(self):
"""
:return: base at current Reference position
"""
return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupGetReferenceBase, c_char).decode("utf-8")
# ----------------------------------------------------------------------
# details of this pileup row
def getPileupDepth(self):
"""
:returns: the coverage depth at the current reference position
"""
return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupGetPileupDepth, c_uint32)
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