mirror of
https://github.com/pcvolkmer/fastq-tools.git
synced 2025-09-13 05:02:53 +00:00
refactor: add FASTQ header subtypes
This commit is contained in:
198
src/fastq.rs
198
src/fastq.rs
@@ -2,7 +2,11 @@ use crate::scramble_sequence;
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use std::fmt::Display;
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use std::str::FromStr;
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pub struct Header {
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pub enum Header {
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Casava18(Casava18Header),
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}
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pub struct Casava18Header {
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instrument_name: String,
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run_id: u32,
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flowcell_id: String,
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@@ -33,45 +37,54 @@ impl Header {
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((value.len() as u8) + value.chars().map(|c| c as u8 & 2).sum::<u8>()) % 97
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}
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Header {
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instrument_name: format!("TEST{:0<2}", (string_sum(&self.instrument_name) * 17) % 97),
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run_id: number(self.run_id),
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flowcell_id: string(&self.flowcell_id),
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flowcell_lane: number(self.flowcell_lane),
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tile_number: number(self.tile_number),
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x: self.x + string_sum(&self.instrument_name) as u32,
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y: self.y + string_sum(&self.instrument_name) as u32,
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pair_member: self.pair_member,
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filtered: self.filtered,
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control_bits: self.control_bits,
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index_sequence: scramble_sequence(&self.index_sequence, 1),
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match self {
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Header::Casava18(header) => Header::Casava18(Casava18Header {
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instrument_name: format!(
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"TEST{:0<2}",
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(string_sum(&header.instrument_name) * 17) % 97
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),
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run_id: number(header.run_id),
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flowcell_id: string(&header.flowcell_id),
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flowcell_lane: number(header.flowcell_lane),
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tile_number: number(header.tile_number),
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x: header.x + string_sum(&header.instrument_name) as u32,
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y: header.y + string_sum(&header.instrument_name) as u32,
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pair_member: header.pair_member,
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filtered: header.filtered,
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control_bits: header.control_bits,
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index_sequence: scramble_sequence(&header.index_sequence, 1),
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}),
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}
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}
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}
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impl Display for Header {
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fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
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write!(
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f,
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"@{}:{}:{}:{}:{}:{}:{} {}:{}:{}:{}",
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self.instrument_name,
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self.run_id,
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self.flowcell_id,
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self.flowcell_lane,
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self.tile_number,
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self.x,
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self.y,
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match self.pair_member {
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Pair::PairedEnd => "1",
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Pair::MatePair => "2",
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},
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match self.filtered {
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Filtered::Y => "Y",
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Filtered::N => "N",
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},
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self.control_bits,
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self.index_sequence
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)
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match self {
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Header::Casava18(header) => {
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write!(
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f,
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"@{}:{}:{}:{}:{}:{}:{} {}:{}:{}:{}",
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header.instrument_name,
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header.run_id,
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header.flowcell_id,
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header.flowcell_lane,
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header.tile_number,
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header.x,
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header.y,
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match header.pair_member {
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Pair::PairedEnd => "1",
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Pair::MatePair => "2",
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},
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match header.filtered {
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Filtered::Y => "Y",
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Filtered::N => "N",
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},
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header.control_bits,
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header.index_sequence
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)
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}
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}
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}
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}
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@@ -80,57 +93,58 @@ impl FromStr for Header {
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fn from_str(s: &str) -> Result<Self, Self::Err> {
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if !s.starts_with("@") {
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return Err("Invalid Casava 1.8+ header".to_string());
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return Err("Cannot parse FASTQ header".to_string());
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}
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let parts = s
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.split(" ")
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.flat_map(|main_part| main_part.split(":").collect::<Vec<_>>())
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.collect::<Vec<_>>();
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if parts.len() != 11 {
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return Err("Invalid Casava 1.8+ header".to_string());
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if parts.len() == 11 {
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return Ok(Header::Casava18(Casava18Header {
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instrument_name: parts[0][1..].to_string(),
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run_id: parts[1]
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.parse()
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.expect("Valid Casava 1.8+ header: Number value required"),
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flowcell_id: parts[2].into(),
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flowcell_lane: parts[3]
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.parse()
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.expect("Valid Casava 1.8+ header: Number value required"),
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tile_number: parts[4]
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.parse()
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.expect("Valid Casava 1.8+ header: Number value required"),
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x: parts[5]
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.parse()
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.expect("Valid Casava 1.8+ header: Number value required"),
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y: parts[6]
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.parse()
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.expect("Valid Casava 1.8+ header: Number value required"),
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pair_member: match parts[7] {
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"1" => Pair::PairedEnd,
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"2" => Pair::MatePair,
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_ => return Err("Invalid Casava 1.8+ header".to_string()),
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},
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filtered: match parts[8] {
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"Y" => Filtered::Y,
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"N" => Filtered::N,
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_ => return Err("Invalid Casava 1.8+ header".to_string()),
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},
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control_bits: if parts[9]
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.parse::<u32>()
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.expect("Valid Casava 1.8+ header: Even value for control bits required")
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% 2
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== 0
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{
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parts[9].parse().expect("Number")
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} else {
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return Err("Invalid Casava 1.8+ header".to_string());
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},
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index_sequence: parts[10].into(),
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}));
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}
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Ok(Header {
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instrument_name: parts[0][1..].to_string(),
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run_id: parts[1]
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.parse()
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.expect("Valid Casava 1.8+ header: Number value required"),
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flowcell_id: parts[2].into(),
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flowcell_lane: parts[3]
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.parse()
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.expect("Valid Casava 1.8+ header: Number value required"),
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tile_number: parts[4]
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.parse()
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.expect("Valid Casava 1.8+ header: Number value required"),
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x: parts[5]
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.parse()
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.expect("Valid Casava 1.8+ header: Number value required"),
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y: parts[6]
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.parse()
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.expect("Valid Casava 1.8+ header: Number value required"),
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pair_member: match parts[7] {
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"1" => Pair::PairedEnd,
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"2" => Pair::MatePair,
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_ => return Err("Invalid Casava 1.8+ header".to_string()),
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},
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filtered: match parts[8] {
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"Y" => Filtered::Y,
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"N" => Filtered::N,
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_ => return Err("Invalid Casava 1.8+ header".to_string()),
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},
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control_bits: if parts[9]
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.parse::<u32>()
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.expect("Valid Casava 1.8+ header: Even value for control bits required")
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% 2
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== 0
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{
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parts[9].parse().expect("Number")
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} else {
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return Err("Invalid Casava 1.8+ header".to_string());
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},
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index_sequence: parts[10].into(),
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})
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Err("Cannot parse FASTQ header".to_string())
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}
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}
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@@ -154,22 +168,22 @@ mod tests {
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#[test]
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fn should_return_parsed_header() {
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let given = "@EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG";
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let actual = given.parse::<Header>();
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assert!(actual.is_ok());
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let actual = actual.unwrap();
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assert_eq!(actual.instrument_name, "EAS139");
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assert_eq!(actual.run_id, 136);
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assert_eq!(actual.flowcell_id, "FC706VJ");
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assert_eq!(actual.flowcell_lane, 2);
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assert_eq!(actual.tile_number, 2104);
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assert_eq!(actual.x, 15343);
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assert_eq!(actual.y, 197393);
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assert_eq!(actual.pair_member, Pair::PairedEnd);
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assert_eq!(actual.filtered, Filtered::Y);
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assert_eq!(actual.control_bits, 18);
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assert_eq!(actual.index_sequence, "ATCACG");
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if let Ok(Header::Casava18(actual)) = given.parse::<Header>() {
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assert_eq!(actual.instrument_name, "EAS139");
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assert_eq!(actual.run_id, 136);
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assert_eq!(actual.flowcell_id, "FC706VJ");
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assert_eq!(actual.flowcell_lane, 2);
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assert_eq!(actual.tile_number, 2104);
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assert_eq!(actual.x, 15343);
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assert_eq!(actual.y, 197393);
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assert_eq!(actual.pair_member, Pair::PairedEnd);
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assert_eq!(actual.filtered, Filtered::Y);
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assert_eq!(actual.control_bits, 18);
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assert_eq!(actual.index_sequence, "ATCACG");
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} else {
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panic!("Failed to parse FASTQ header");
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}
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}
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#[test]
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