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1 from cpython cimport bool
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2 from libcpp.vector cimport vector
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3 from libcpp.string cimport string
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4 from cython.operator cimport dereference as deref
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5
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6
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7
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8
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9
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10
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11 """
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12 Create Cython definitions for the Interval API defined in Interval.h
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13 """
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14 cdef extern from "bedFile.h":
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15 cdef enum BedLineStatus:
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16 BED_MALFORMED = -2
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17 BED_INVALID = -1
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18 BED_HEADER = 0
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19 BED_BLANK = 1
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20 BED_VALID = 2
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21
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22 ctypedef unsigned int CHRPOS
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23 ctypedef bint BOOL
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24
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25 cdef cppclass BED:
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26 string chrom
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27 CHRPOS start
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28 CHRPOS end
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29 string name
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30 string score
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31 string strand
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32 CHRPOS o_start # the start of an overlap with another interval
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33 CHRPOS o_end # the end of an overlap with another interval
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34 unsigned short bedType
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35 string file_type
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36 BedLineStatus status
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37 vector[string] fields
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38
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39 # constructors
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40 BED()
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41 BED(string chrom, CHRPOS start, CHRPOS end, string name,
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42 string score, string strand, vector[string] fields,
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43 CHRPOS o_start, CHRPOS o_end,
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44 unsigned short bedType, string file_type, BedLineStatus status)
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45
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46 BED(string chrom, CHRPOS start, CHRPOS end)
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47 BED(string chrom, CHRPOS start, CHRPOS end, string strand)
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48 BED(string chrom, CHRPOS start, CHRPOS end, string name,
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49 string score, string strand, vector[string] fields)
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50
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51 # methods
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52 string reportBed()
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53
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54
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55 cdef cppclass BedFile:
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56 BedFile(string)
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57 int Open()
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58 void Rewind()
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59 void Seek(unsigned long offset)
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60 void Close()
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61 BED GetNextBed()
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62 void loadBedFileIntoMap()
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63
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64 ### "all" ###
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65 # this version doesn't care if the strands match.
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66 vector[BED] FindOverlapsPerBin(BED bed, float overlapFraction)
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67 # if forceStrand is true, require that the strands match,
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68 vector[BED] FindOverlapsPerBin(BED bed, bool forceStrand, float overlapFraction)
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69
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70 ### "any" ###
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71 int FindAnyOverlapsPerBin(BED bed, float overlapFraction)
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72 # if forceStrand is true, require that the strands match,
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73 int FindAnyOverlapsPerBin(BED bed, bool forceStrand, float overlapFraction)
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74
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75
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76 ### "count" ###
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77 int CountOverlapsPerBin(BED bed, float overlapFraction)
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78 # if forceStrand is true, require that the strands match,
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79 int CountOverlapsPerBin(BED bed, bool forceStrand, float overlapFraction)
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80 string file_type
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81 bint _typeIsKnown
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82
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83
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84 cdef class Interval:
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85 cdef BED *_bed
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86 cdef object _attrs
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87 cpdef append(Interval self, object value)
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88 cpdef deparse_attrs(Interval self)
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