Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pybedtools/cbedtools.pxd @ 68:5028fdace37b
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 16:23:26 -0400 |
| parents | |
| children |
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| 67:0e9998148a16 | 68:5028fdace37b |
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| 1 from cpython cimport bool | |
| 2 from libcpp.vector cimport vector | |
| 3 from libcpp.string cimport string | |
| 4 from cython.operator cimport dereference as deref | |
| 5 | |
| 6 | |
| 7 | |
| 8 | |
| 9 | |
| 10 | |
| 11 """ | |
| 12 Create Cython definitions for the Interval API defined in Interval.h | |
| 13 """ | |
| 14 cdef extern from "bedFile.h": | |
| 15 cdef enum BedLineStatus: | |
| 16 BED_MALFORMED = -2 | |
| 17 BED_INVALID = -1 | |
| 18 BED_HEADER = 0 | |
| 19 BED_BLANK = 1 | |
| 20 BED_VALID = 2 | |
| 21 | |
| 22 ctypedef unsigned int CHRPOS | |
| 23 ctypedef bint BOOL | |
| 24 | |
| 25 cdef cppclass BED: | |
| 26 string chrom | |
| 27 CHRPOS start | |
| 28 CHRPOS end | |
| 29 string name | |
| 30 string score | |
| 31 string strand | |
| 32 CHRPOS o_start # the start of an overlap with another interval | |
| 33 CHRPOS o_end # the end of an overlap with another interval | |
| 34 unsigned short bedType | |
| 35 string file_type | |
| 36 BedLineStatus status | |
| 37 vector[string] fields | |
| 38 | |
| 39 # constructors | |
| 40 BED() | |
| 41 BED(string chrom, CHRPOS start, CHRPOS end, string name, | |
| 42 string score, string strand, vector[string] fields, | |
| 43 CHRPOS o_start, CHRPOS o_end, | |
| 44 unsigned short bedType, string file_type, BedLineStatus status) | |
| 45 | |
| 46 BED(string chrom, CHRPOS start, CHRPOS end) | |
| 47 BED(string chrom, CHRPOS start, CHRPOS end, string strand) | |
| 48 BED(string chrom, CHRPOS start, CHRPOS end, string name, | |
| 49 string score, string strand, vector[string] fields) | |
| 50 | |
| 51 # methods | |
| 52 string reportBed() | |
| 53 | |
| 54 | |
| 55 cdef cppclass BedFile: | |
| 56 BedFile(string) | |
| 57 int Open() | |
| 58 void Rewind() | |
| 59 void Seek(unsigned long offset) | |
| 60 void Close() | |
| 61 BED GetNextBed() | |
| 62 void loadBedFileIntoMap() | |
| 63 | |
| 64 ### "all" ### | |
| 65 # this version doesn't care if the strands match. | |
| 66 vector[BED] FindOverlapsPerBin(BED bed, float overlapFraction) | |
| 67 # if forceStrand is true, require that the strands match, | |
| 68 vector[BED] FindOverlapsPerBin(BED bed, bool forceStrand, float overlapFraction) | |
| 69 | |
| 70 ### "any" ### | |
| 71 int FindAnyOverlapsPerBin(BED bed, float overlapFraction) | |
| 72 # if forceStrand is true, require that the strands match, | |
| 73 int FindAnyOverlapsPerBin(BED bed, bool forceStrand, float overlapFraction) | |
| 74 | |
| 75 | |
| 76 ### "count" ### | |
| 77 int CountOverlapsPerBin(BED bed, float overlapFraction) | |
| 78 # if forceStrand is true, require that the strands match, | |
| 79 int CountOverlapsPerBin(BED bed, bool forceStrand, float overlapFraction) | |
| 80 string file_type | |
| 81 bint _typeIsKnown | |
| 82 | |
| 83 | |
| 84 cdef class Interval: | |
| 85 cdef BED *_bed | |
| 86 cdef object _attrs | |
| 87 cpdef append(Interval self, object value) | |
| 88 cpdef deparse_attrs(Interval self) |