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feat: Add error codes #257

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feat: Add error codes #257

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2 changes: 1 addition & 1 deletion src/read_pair.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ impl ReadOffset {
/// 'primary' reads, I1 and I2 are the two 'index' samples. I1 is
/// often referred to as the 'sample index read', or I7. I2 contains
/// the 10x barcode sequence in some 10x assays.
#[derive(Serialize, Deserialize, Copy, Clone, Eq, PartialEq, Hash, Debug)]
#[derive(Serialize, Deserialize, Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug)]
pub enum WhichRead {
R1 = 0,
R2 = 1,
Expand Down
80 changes: 44 additions & 36 deletions src/read_pair_iter.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ use rand::SeedableRng;
use rand_xorshift::XorShiftRng;
use serde::{Deserialize, Serialize};
use std::io::{self, BufRead, BufReader, ErrorKind, Read, Seek, Write};
use std::iter::zip;
use std::ops::DerefMut;
use std::path::{Path, PathBuf};
use thiserror::Error;
Expand All @@ -25,10 +26,10 @@ pub enum FastqError {
file: PathBuf,
},

#[error("Error opening FASTQ file '{}'", file.display())]
#[error("TENX1200001: Error opening FASTQ file: '{}'", file.display())]
Open { file: PathBuf, source: io::Error },

#[error("IO error in FASTQ file '{}', line: {line}", file.display())]
#[error("TENX1200002: IO error in FASTQ file: '{}', line: {line}", file.display())]
Io {
file: PathBuf,
line: usize,
Expand All @@ -48,13 +49,13 @@ impl FastqError {
}

trait FileIoError<T> {
fn open_err(self, path: impl Into<PathBuf>) -> Result<T, FastqError>;
fn fastq_err(self, path: impl Into<PathBuf>, line: usize) -> Result<T, FastqError>;
fn open_err(self, path: &Path) -> Result<T, FastqError>;
fn fastq_err(self, path: &Path, line: usize) -> Result<T, FastqError>;
}

impl<T> FileIoError<T> for Result<T, std::io::Error> {
#[cold]
fn open_err(self, path: impl Into<PathBuf>) -> Result<T, FastqError> {
fn open_err(self, path: &Path) -> Result<T, FastqError> {
match self {
Ok(v) => Ok(v),
Err(e) => {
Expand All @@ -68,20 +69,20 @@ impl<T> FileIoError<T> for Result<T, std::io::Error> {
}

#[cold]
fn fastq_err(self, path: impl Into<PathBuf>, line: usize) -> Result<T, FastqError> {
fn fastq_err(self, path: &Path, line: usize) -> Result<T, FastqError> {
match self {
Ok(v) => Ok(v),
Err(e) => {
match e.kind() {
// convert InvalidData into a FastqFormat error
ErrorKind::InvalidData => Err(FastqError::FastqFormat {
message: e.to_string(),
message: format!("TENX1200003: {e}"),
line,
file: path.into(),
file: PathBuf::from(path),
}),
// convert everything else to the Io case
_ => Err(FastqError::Io {
file: path.into(),
file: PathBuf::from(path),
line,
source: e,
}),
Expand Down Expand Up @@ -502,34 +503,41 @@ impl ReadPairIter {
}
}

// check that headers of all reads match
let mut header_slices = Vec::with_capacity(4);

for (i, w) in [WhichRead::R1, WhichRead::R2, WhichRead::I1, WhichRead::I2]
.iter()
.enumerate()
{
if let Some(header) = rp.get(*w, ReadPart::Header) {
let prefix = header.split(|x| *x == b' ' || *x == b'/').next();
header_slices.push((i, prefix));
}
}
// Check that headers of all reads match.
let mut headers = zip(
[WhichRead::R1, WhichRead::R2, WhichRead::I1, WhichRead::I2],
rec_num.iter().copied(),
)
.filter_map(|(which_read, this_rec_num)| {
rp.get(which_read, ReadPart::Header).map(|header| {
(
which_read,
this_rec_num,
header.split(|&x| matches!(x, b' ' | b'/')).next(),
)
})
});

if !header_slices.is_empty() {
for i in 1..header_slices.len() {
if header_slices[i].1 != header_slices[0].1 {
let msg = format!("FASTQ header mismatch detected at line {} of input files {:?} and {:?}",
rec_num[0] * 4,
paths[header_slices[0].0].as_ref().unwrap(),
paths[header_slices[i].0].as_ref().unwrap()
);

let e = FastqError::format(
msg,
paths[header_slices[0].0].as_ref().unwrap(),
rec_num[i] * 4,
);
return Err(e);
if let Some((first_which_read, first_rec_num, first_header)) = headers.next() {
for (this_which_read, this_rec_num, this_header) in headers {
if first_header != this_header {
let first_path = paths[first_which_read as usize].as_ref().unwrap();
let this_path = paths[this_which_read as usize].as_ref().unwrap();
return Err(FastqError::format(
format!(
"TENX1200004: FASTQ headers do not match at line {} of input files \
'{}' and '{}': '{}' and '{}'",
4 * first_rec_num,
first_path.display(),
this_path.display(),
first_header.map_or(String::new(), |s| String::from_utf8_lossy(s)
.to_string()),
this_header.map_or(String::new(), |s| String::from_utf8_lossy(s)
.to_string()),
),
first_path,
4 * this_rec_num,
));
}
}
}
Expand Down
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