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from cpython cimport bool
from libcpp.vector cimport vector
from libcpp.string cimport string
from cython.operator cimport dereference as deref
"""
Create Cython definitions for the Interval API defined in Interval.h
"""
cdef extern from "bedFile.h":
cdef enum BedLineStatus:
BED_MALFORMED = -2
BED_INVALID = -1
BED_HEADER = 0
BED_BLANK = 1
BED_VALID = 2
ctypedef unsigned int CHRPOS
ctypedef bint BOOL
cdef cppclass BED:
string chrom
CHRPOS start
CHRPOS end
string name
string score
string strand
CHRPOS o_start # the start of an overlap with another interval
CHRPOS o_end # the end of an overlap with another interval
unsigned short bedType
string file_type
BedLineStatus status
vector[string] fields
# constructors
BED()
BED(string chrom, CHRPOS start, CHRPOS end, string name,
string score, string strand, vector[string] fields,
CHRPOS o_start, CHRPOS o_end,
unsigned short bedType, string file_type, BedLineStatus status)
BED(string chrom, CHRPOS start, CHRPOS end)
BED(string chrom, CHRPOS start, CHRPOS end, string strand)
BED(string chrom, CHRPOS start, CHRPOS end, string name,
string score, string strand, vector[string] fields)
# methods
string reportBed()
cdef cppclass BedFile:
BedFile(string)
int Open()
void Rewind()
void Seek(unsigned long offset)
void Close()
BED GetNextBed()
void loadBedFileIntoMap()
### "all" ###
# this version doesn't care if the strands match.
vector[BED] FindOverlapsPerBin(BED bed, float overlapFraction)
# if forceStrand is true, require that the strands match,
vector[BED] FindOverlapsPerBin(BED bed, bool forceStrand, float overlapFraction)
### "any" ###
int FindAnyOverlapsPerBin(BED bed, float overlapFraction)
# if forceStrand is true, require that the strands match,
int FindAnyOverlapsPerBin(BED bed, bool forceStrand, float overlapFraction)
### "count" ###
int CountOverlapsPerBin(BED bed, float overlapFraction)
# if forceStrand is true, require that the strands match,
int CountOverlapsPerBin(BED bed, bool forceStrand, float overlapFraction)
string file_type
bint _typeIsKnown
cdef class Interval:
cdef BED *_bed
cdef object _attrs
cpdef append(Interval self, object value)
cpdef deparse_attrs(Interval self)
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