noodles_csi/binning_index/index/reference_sequence/
metadata.rs

1use noodles_bgzf as bgzf;
2
3use super::bin::Chunk;
4
5/// Index reference sequence metadata.
6#[derive(Clone, Debug, Eq, PartialEq)]
7pub struct Metadata {
8    start_position: bgzf::VirtualPosition,
9    end_position: bgzf::VirtualPosition,
10    mapped_record_count: u64,
11    unmapped_record_count: u64,
12}
13
14impl Metadata {
15    /// Creates reference sequence metadata.
16    ///
17    /// # Examples
18    ///
19    /// ```
20    /// use noodles_bgzf as bgzf;
21    /// use noodles_csi::binning_index::index::reference_sequence::Metadata;
22    ///
23    /// let metadata = Metadata::new(
24    ///     bgzf::VirtualPosition::from(610),
25    ///     bgzf::VirtualPosition::from(1597),
26    ///     55,
27    ///     0,
28    /// );
29    /// ```
30    pub fn new(
31        start_position: bgzf::VirtualPosition,
32        end_position: bgzf::VirtualPosition,
33        mapped_record_count: u64,
34        unmapped_record_count: u64,
35    ) -> Self {
36        Self {
37            start_position,
38            end_position,
39            mapped_record_count,
40            unmapped_record_count,
41        }
42    }
43
44    /// Returns the start virtual position.
45    ///
46    /// # Examples
47    ///
48    /// ```
49    /// use noodles_bgzf as bgzf;
50    /// use noodles_csi::binning_index::index::reference_sequence::Metadata;
51    ///
52    /// let metadata = Metadata::new(
53    ///     bgzf::VirtualPosition::from(610),
54    ///     bgzf::VirtualPosition::from(1597),
55    ///     55,
56    ///     0,
57    /// );
58    ///
59    /// assert_eq!(metadata.start_position(), bgzf::VirtualPosition::from(610));
60    /// ```
61    pub fn start_position(&self) -> bgzf::VirtualPosition {
62        self.start_position
63    }
64
65    /// Returns the end virtual position.
66    ///
67    /// # Examples
68    ///
69    /// ```
70    /// use noodles_bgzf as bgzf;
71    /// use noodles_csi::binning_index::index::reference_sequence::Metadata;
72    ///
73    /// let metadata = Metadata::new(
74    ///     bgzf::VirtualPosition::from(610),
75    ///     bgzf::VirtualPosition::from(1597),
76    ///     55,
77    ///     0,
78    /// );
79    ///
80    /// assert_eq!(metadata.end_position(), bgzf::VirtualPosition::from(1597));
81    /// ```
82    pub fn end_position(&self) -> bgzf::VirtualPosition {
83        self.end_position
84    }
85
86    /// Returns the number of mapped records.
87    ///
88    /// # Examples
89    ///
90    /// ```
91    /// use noodles_bgzf as bgzf;
92    /// use noodles_csi::binning_index::index::reference_sequence::Metadata;
93    ///
94    /// let metadata = Metadata::new(
95    ///     bgzf::VirtualPosition::from(610),
96    ///     bgzf::VirtualPosition::from(1597),
97    ///     55,
98    ///     0,
99    /// );
100    ///
101    /// assert_eq!(metadata.mapped_record_count(), 55);
102    /// ```
103    pub fn mapped_record_count(&self) -> u64 {
104        self.mapped_record_count
105    }
106
107    /// Returns the number of unmapped records.
108    ///
109    /// # Examples
110    ///
111    /// ```
112    /// use noodles_bgzf as bgzf;
113    /// use noodles_csi::binning_index::index::reference_sequence::Metadata;
114    ///
115    /// let metadata = Metadata::new(
116    ///     bgzf::VirtualPosition::from(610),
117    ///     bgzf::VirtualPosition::from(1597),
118    ///     55,
119    ///     0,
120    /// );
121    ///
122    /// assert_eq!(metadata.unmapped_record_count(), 0);
123    /// ```
124    pub fn unmapped_record_count(&self) -> u64 {
125        self.unmapped_record_count
126    }
127
128    pub(super) fn update(&mut self, is_mapped: bool, chunk: Chunk) {
129        if is_mapped {
130            self.mapped_record_count += 1;
131        } else {
132            self.unmapped_record_count += 1;
133        }
134
135        self.start_position = self.start_position.min(chunk.start());
136        self.end_position = self.end_position.max(chunk.end());
137    }
138}
noodles_csi/binning_index/index/reference_sequence/metadata.rs

noodles_csi/binning_index/index/reference_sequence/
metadata.rs
