/usr/lib/python2.7/dist-packages/ngs/PileupEvent.py is in python-ngs 1.3.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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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
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
#
#
from ctypes import c_char, c_int32, c_uint32, c_int64, c_void_p
from . import NGS
from .String import getNGSString, getNGSValue
from .Refcount import Refcount
from .Alignment import Alignment
# Represents a single cell of a sparse 2D matrix with Reference coordinates on one axis
# and stacked Alignments on the other axis
class PileupEvent(Refcount):
# ----------------------------------------------------------------------
# Reference
def getMappingQuality(self):
return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetMappingQuality, c_int32)
# ----------------------------------------------------------------------
# Alignment
def getAlignmentId(self):
return getNGSString(self, NGS.lib_manager.PY_NGS_PileupEventGetAlignmentId)
def getAlignmentPosition(self):
return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetAlignmentPosition, c_int64)
def getFirstAlignmentPosition(self):
"""
:returns: the position of this Alignment's first event in Reference coordinates
"""
return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetFirstAlignmentPosition, c_int64)
def getLastAlignmentPosition(self):
"""
:returns: the position of this Alignment's last event in INCLUSIVE Reference coordinates
"""
return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetLastAlignmentPosition, c_int64)
# ----------------------------------------------------------------------
# event details
match = 0
mismatch = 1
deletion = 2
# an insertion cannot be represented in reference coordinate
# space ( so no insertion event can be directly represented ),
# but it can occur before a match or mismatch event.
# insertion is represented as a bit
insertion = 0x08
# insertions into the reference
insertion_before_match = insertion | match
insertion_before_mismatch = insertion | mismatch
# simultaneous insertion and deletion,
# a.k.a. a replacement
insertion_before_deletion = insertion | deletion
replacement = insertion_before_deletion
# additional modifier bits - may be added to any event above
alignment_start = 0x80
alignment_stop = 0x40
alignment_minus_strand = 0x20
def getEventType(self):
return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetEventType, c_uint32)
def getAlignmentBase(self):
"""
:returns: retrieves base aligned at current Reference position
:throws: ErrorMsg if event is an insertion or deletion
"""
return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetAlignmentBase, c_char).decode("utf-8")
def getAlignmentQuality(self):
"""
:returns: retrieves base aligned at current Reference position
:throws: ErrorMsg if event is an insertion or deletion
"""
return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetAlignmentQuality, c_char).decode("utf-8")
def getInsertionBases(self):
"""
:returns: bases corresponding to insertion event
"""
return getNGSString(self, NGS.lib_manager.PY_NGS_PileupEventGetInsertionBases)
def getInsertionQualities(self):
"""
:returns: qualities corresponding to insertion event
"""
return getNGSString(self, NGS.lib_manager.PY_NGS_PileupEventGetInsertionQualities)
def getEventRepeatCount(self):
"""
:returns: the number of times this event repeats, i.e. the distance to the first reference position yielding a different event type for this alignment
"""
return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetEventRepeatCount, c_uint32)
# EventIndelType
normal_indel = 0
# introns behave like deletions
# (i.e. can retrieve deletion count),
# "_plus" and "_minus" signify direction
# of transcription if known
intron_plus = 1
intron_minus = 2
intron_unknown = 3
# overlap is reported as an insertion,
# but is actually an overlap in the read
# inherent in technology like Complete Genomics
read_overlap = 4
# gap is reported as a deletion,
# but is actually a gap in the read
# inherent in technology like Complete Genomics
read_gap = 5
def getEvenIndeltType(self):
return getNGSValue(self, NGS.lib_manager.PY_NGS_PileupEventGetEventIndelType, c_uint32)
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