jpayne@68: from cpython cimport bool
jpayne@68: from libcpp.vector cimport vector
jpayne@68: from libcpp.string cimport string
jpayne@68: from cython.operator cimport dereference as deref
jpayne@68: 
jpayne@68: 
jpayne@68: 
jpayne@68: 
jpayne@68: 
jpayne@68: 
jpayne@68: """
jpayne@68: Create Cython definitions for the Interval API defined in Interval.h
jpayne@68: """
jpayne@68: cdef extern from "bedFile.h":
jpayne@68:     cdef enum BedLineStatus:
jpayne@68:         BED_MALFORMED = -2
jpayne@68:         BED_INVALID = -1
jpayne@68:         BED_HEADER = 0
jpayne@68:         BED_BLANK = 1
jpayne@68:         BED_VALID = 2
jpayne@68: 
jpayne@68:     ctypedef unsigned int   CHRPOS
jpayne@68:     ctypedef bint BOOL
jpayne@68: 
jpayne@68:     cdef cppclass BED:
jpayne@68:         string chrom
jpayne@68:         CHRPOS start
jpayne@68:         CHRPOS end
jpayne@68:         string name
jpayne@68:         string score
jpayne@68:         string strand
jpayne@68:         CHRPOS o_start  # the start of an overlap with another interval
jpayne@68:         CHRPOS o_end    # the end of an overlap with another interval
jpayne@68:         unsigned short bedType
jpayne@68:         string file_type
jpayne@68:         BedLineStatus status
jpayne@68:         vector[string] fields
jpayne@68: 
jpayne@68:         # constructors
jpayne@68:         BED()
jpayne@68:         BED(string chrom, CHRPOS start, CHRPOS end, string name,
jpayne@68:              string score, string strand, vector[string] fields,
jpayne@68:              CHRPOS o_start, CHRPOS o_end,
jpayne@68:              unsigned short bedType, string file_type, BedLineStatus status)
jpayne@68: 
jpayne@68:         BED(string chrom, CHRPOS start, CHRPOS end)
jpayne@68:         BED(string chrom, CHRPOS start, CHRPOS end, string strand)
jpayne@68:         BED(string chrom, CHRPOS start, CHRPOS end, string name,
jpayne@68:              string score, string strand, vector[string] fields)
jpayne@68: 
jpayne@68:         # methods
jpayne@68:         string reportBed()
jpayne@68: 
jpayne@68: 
jpayne@68:     cdef cppclass BedFile:
jpayne@68:         BedFile(string)
jpayne@68:         int Open()
jpayne@68:         void Rewind()
jpayne@68:         void Seek(unsigned long offset)
jpayne@68:         void Close()
jpayne@68:         BED  GetNextBed()
jpayne@68:         void loadBedFileIntoMap()
jpayne@68: 
jpayne@68:         ### "all" ###
jpayne@68:         # this version doesn't care if the strands match.
jpayne@68:         vector[BED] FindOverlapsPerBin(BED bed, float overlapFraction)
jpayne@68:         # if forceStrand is true, require that the strands match,
jpayne@68:         vector[BED] FindOverlapsPerBin(BED bed, bool forceStrand, float overlapFraction)
jpayne@68: 
jpayne@68:         ### "any" ###
jpayne@68:         int FindAnyOverlapsPerBin(BED bed, float overlapFraction)
jpayne@68:         # if forceStrand is true, require that the strands match,
jpayne@68:         int FindAnyOverlapsPerBin(BED bed, bool forceStrand, float overlapFraction)
jpayne@68: 
jpayne@68: 
jpayne@68:         ### "count" ###
jpayne@68:         int CountOverlapsPerBin(BED bed, float overlapFraction)
jpayne@68:         # if forceStrand is true, require that the strands match,
jpayne@68:         int CountOverlapsPerBin(BED bed, bool forceStrand, float overlapFraction)
jpayne@68:         string file_type
jpayne@68:         bint _typeIsKnown
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class Interval:
jpayne@68:     cdef BED *_bed
jpayne@68:     cdef object _attrs
jpayne@68:     cpdef append(Interval self, object value)
jpayne@68:     cpdef deparse_attrs(Interval self)