rsvart 0.1.5

A small library for representing genomic variants and regions.
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144

use crate::{Contiged, GenomicRegion, Regioned};
use crate::stranded::Stranded;

pub trait StrandedContigedRegioned<T> {
    fn contains(&self, other: &U) -> bool;

    fn overlaps_with(&self, other: &U) -> bool;

    fn overlap_length(&self, other: &U) -> u32;

    fn distance_to(&self) -> u32;

    fn start_on_strand(&self) -> u32;
    
    fn end_on_strand(&self) -> u32;

}

impl <T: Regioned + Stranded + Contiged, U: Regioned + Stranded + Contiged> StrandedContigedRegioned<T, U> for T {
    fn contains(&self, other: &U) -> bool {
        
        if self.contig().id() != other.contig().id() {
            return false;
        }

        if self.strand() == other.strand() {
            return self.region().contains(other.region());
        }
        // TODO: If strands are not the same we need to do something here.
        return false;
    }

    //        if (this.contigId() != other.contigId()) {
    //             return false;
    //         }
    //         if (this.strand() == other.strand()) {
    //             return this.coordinates().overlaps(other.coordinates());
    //         }
    //         int otherStart = other.startOnStrand(this.strand());
    //         int otherEnd = other.endOnStrand(this.strand());
    //         return this.coordinates().overlaps(other.coordinateSystem(), otherStart, otherEnd);
    //     }
    fn overlaps_with(&self, other: &U) -> bool {
        if self.contig() != other.contig()  {
            return false;
        }
        
        if self.strand() == other.strand() {
            return self.region().overlaps()
        }
        
        todo!()
    }

    fn overlap_length(&self, other: &U) -> u32 {
        todo!()
    }

    fn distance_to(&self) -> u32 {
        todo!()
    }

    fn start_on_strand(&self) -> u32 {
        todo!()
    }

    fn end_on_strand(&self) -> u32 {
        todo!()
    }
}


#[cfg(test)]
mod test {
    use std::rc::Rc;
    use super::*;
    use crate::{AssignedMoleculeType, Contig, CoordinateSystem, SequenceRole, Strand};
    use crate::Region;
    use rstest::rstest;
    
    fn contigs() -> (Contig, Contig) {
        (
            Contig::new(1, "1".to_string(), SequenceRole::AssembledMolecule, "1".to_string(), AssignedMoleculeType::Chromosome, 249_250_621, "CM000663.1".to_string(), "NC_000001.10".to_string(), "chr1".to_string()).unwrap(),
            Contig::new(2, "2".to_string(), SequenceRole::AssembledMolecule, "1".to_string(), AssignedMoleculeType::Chromosome, 249_250_621, "CM000663.1".to_string(), "NC_000001.10".to_string(), "chr1".to_string()).unwrap()    
        )
    }
    
    fn region(index: u8) -> TestRegion {
        let (contig_1, contig_2) = contigs();
        match index {
            1 => TestRegion { strand: Strand::Positive,
                region: Region::new(0,20, CoordinateSystem::zero_based()), contig: Rc::new(contig_1.clone())
            },
            2 => TestRegion { strand: Strand::Positive,
                region: Region::new(13, 19, CoordinateSystem::zero_based()), contig: Rc::new(contig_1.clone())
            },
            3 => TestRegion { strand: Strand::Positive,
                region: Region::new(21, 36, CoordinateSystem::zero_based()), contig: Rc::new(contig_1.clone())
            },
            4 =>  TestRegion { strand: Strand::Negative,
                region: Region::new(21, 36, CoordinateSystem::zero_based()), contig: Rc::new(contig_1.clone())
            },
            5 => TestRegion { strand: Strand::Positive,
                region: Region::new(21, 36, CoordinateSystem::zero_based()), contig: Rc::new(contig_2.clone())
            },
            _ => panic!("Test setup not right")
        }
    }
    
    struct TestRegion {
        strand: Strand,
        region: Region,
        contig: Rc<Contig>
    }

    impl Stranded for TestRegion {
        fn strand(&self) -> Strand {
            return self.strand;
        }
    }

    impl Regioned for TestRegion {
        fn region(&self) -> &Region {
            &self.region
        }
    }

    impl Contiged for TestRegion {
        fn contig(&self) -> &Contig {
            &*self.contig
        }
    }

    #[rstest]
    #[case(region(1), region(2), true)]
    #[case(region(1), region(3), false)]
    #[case(region(1), region(4), false)]
    #[case(region(1), region(5), false)]
    fn test_contains(#[case] input: TestRegion, #[case] other: TestRegion, #[case] expected: bool) {
        assert_eq!(input.contains(&other), expected);
    }
}