bgzip 0.3.1

Rust implementation of bgzip
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
145
146
147
148
149

//! .gzi index support

use std::convert::TryInto;

use crate::{BGZFError, BinaryReader};

/// Represents .gzi index file
#[derive(Debug, Clone, PartialEq, Default)]
pub struct BGZFIndex {
    pub(crate) entries: Vec<BGZFIndexEntry>,
}

impl BGZFIndex {
    pub(crate) fn new() -> Self {
        BGZFIndex::default()
    }

    /// List of index entries
    pub fn entries(&self) -> &[BGZFIndexEntry] {
        &self.entries
    }

    /// Load .gzi index file from `reader`
    pub fn from_reader<R: std::io::Read>(mut reader: R) -> std::io::Result<Self> {
        let num_entries = reader.read_le_u64()?;
        let mut result = BGZFIndex::default();
        for _ in 0..num_entries {
            let compressed_offset = reader.read_le_u64()?;
            let uncompressed_offset = reader.read_le_u64()?;
            result.entries.push(BGZFIndexEntry {
                compressed_offset,
                uncompressed_offset,
            })
        }
        Ok(result)
    }

    /// Write .gzi index file into `writer`
    pub fn write<W: std::io::Write>(&self, mut writer: W) -> std::io::Result<()> {
        let entries: u64 = self.entries.len().try_into().unwrap();
        writer.write_all(&entries.to_le_bytes())?;
        for one in &self.entries {
            writer.write_all(&one.compressed_offset.to_le_bytes())?;
            writer.write_all(&one.uncompressed_offset.to_le_bytes())?;
        }
        Ok(())
    }

    /// Convert uncompressed position to bgzf virtual position
    pub fn uncompressed_pos_to_bgzf_pos(&self, pos: u64) -> Result<u64, BGZFError> {
        let i = self
            .entries
            .partition_point(|x| x.uncompressed_offset <= pos);
        let entry = match i {
            0 => BGZFIndexEntry {
                compressed_offset: 0,
                uncompressed_offset: 0,
            },
            i => self.entries[i - 1].clone(),
        };
        // eprintln!(
        //     "[{}/{}] {} / {} ",
        //     i,
        //     self.entries().len(),
        //     pos,
        //     entry.uncompressed_offset
        // );
        Ok((entry.compressed_offset << 16) + ((pos - entry.uncompressed_offset) & ((1 << 16) - 1)))
    }

    /// Convert bgzf virtual position to uncompressed position
    pub fn bgzf_pos_to_uncompressed_pos(&self, bgzf_pos: u64) -> Result<u64, BGZFError> {
        let compressed_pos = bgzf_pos >> 16;
        if compressed_pos == 0 {
            return Ok(bgzf_pos);
        }
        let i = self
            .entries
            .binary_search_by(|x| x.compressed_offset.cmp(&compressed_pos))
            .map_err(|_| BGZFError::Other("Invalid BGZF position"))?;
        Ok(self.entries[i].uncompressed_offset + (bgzf_pos & ((1 << 16) - 1)))
    }
}

/// One entry of .gzi
#[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord)]
pub struct BGZFIndexEntry {
    pub compressed_offset: u64,
    pub uncompressed_offset: u64,
}

#[cfg(test)]
mod test {
    use super::*;
    use crate::{BGZFWriter, Compression};
    use std::fs;
    use std::io::prelude::*;

    #[test]
    fn test_index_read_write() -> anyhow::Result<()> {
        let data = fs::read("testfiles/generated.bed.gz.gzi")?;
        let index = BGZFIndex::from_reader(&data[..])?;
        assert_eq!(index.entries.len(), 295);
        let mut generated_data = Vec::new();
        index.write(&mut generated_data)?;
        assert_eq!(data, generated_data);

        Ok(())
    }

    #[test]
    fn test_index_position_convert() -> anyhow::Result<()> {
        let mut data_reader = std::io::BufReader::new(flate2::read::MultiGzDecoder::new(
            fs::File::open("testfiles/generated.bed.gz")?,
        ));
        let mut line = String::new();
        let mut line_list = Vec::new();
        let mut writer = BGZFWriter::new(
            fs::File::create("tmp/test_index_position_convert.bed.gz")?,
            Compression::default(),
        );

        loop {
            let bgzf_pos = writer.bgzf_pos();
            let uncompressed_pos = writer.pos();
            line.clear();
            let size = data_reader.read_line(&mut line)?;
            if size == 0 {
                break;
            }
            writer.write_all(&line.as_bytes())?;
            line_list.push((bgzf_pos, uncompressed_pos, line.clone()));
        }
        let index = writer.close()?.unwrap();

        for (bgzf_pos, uncompressed_pos, _) in &line_list {
            assert_eq!(
                index.bgzf_pos_to_uncompressed_pos(*bgzf_pos)?,
                *uncompressed_pos
            );
            assert_eq!(
                index.uncompressed_pos_to_bgzf_pos(*uncompressed_pos)?,
                *bgzf_pos
            );
        }

        Ok(())
    }
}