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try returning no r2 for single ended
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@govinda-kamath
govinda-kamath committed May 25, 2024
1 parent 8f39e91 commit 5ef45b8
Showing 1 changed file with 4 additions and 14 deletions.
18 changes: 4 additions & 14 deletions src/read_pair_iter.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
use crate::read_pair::{MutReadPair, ReadPair, ReadPairStorage, ReadPart, WhichRead};
use bytes::{BufMut, BytesMut};
use fastq::{self, OwnedRecord, Record, RecordRefIter};
use fastq::{self, Record, RecordRefIter};
use rand::distributions::{Distribution, Uniform};
use rand::SeedableRng;
use rand_xorshift::XorShiftRng;
Expand Down Expand Up @@ -406,7 +406,7 @@ impl ReadPairIter {
iter.advance()
.fastq_err(paths[idx].as_ref().unwrap(), rec_num[idx] * 4)?;

let current_read_record = {
{
let record = iter.get();

// Check for non-ACGTN characters
Expand All @@ -433,8 +433,7 @@ impl ReadPairIter {
}

rec_num[idx] += 1;
record
};
}

// If R1 is interleaved, read another entry
// and store it as R2
Expand Down Expand Up @@ -475,16 +474,6 @@ impl ReadPairIter {
}

rec_num[idx] += 1;
} else if let Some(current_read_record) = current_read_record {
let read_length = read_lengths[WhichRead::R2 as usize];
let fake_r2_read = OwnedRecord {
head: current_read_record.head().to_owned(),
sep: Some(current_read_record.seq().to_owned()),
seq: vec![],
qual: vec![],
};
let tr = TrimRecord::new(&fake_r2_read, read_length);
rp.push_read(&tr, WhichRead::R2)
}
}

Check failure on line 478 in src/read_pair_iter.rs

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this `if` statement can be collapsed 

error: this `if` statement can be collapsed
   --> src/read_pair_iter.rs:440:21
    |
440 | /                     if idx == 0 && self.r1_interleaved && !iter_ended[idx] {
441 | |                         if !is_single_ended {
442 | |                             iter.advance()
443 | |                                 .fastq_err(paths[idx].as_ref().unwrap(), (rec_num[idx] + 1) * 4)?;
...   |
477 | |                         }
478 | |                     }
    | |_____________________^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#collapsible_if
note: the lint level is defined here
   --> src/lib.rs:12:9
    |
12  | #![deny(warnings, unused)]
    |         ^^^^^^^^
    = note: `#[deny(clippy::collapsible_if)]` implied by `#[deny(warnings)]`
help: collapse nested if block
    |
440 ~                     if idx == 0 && self.r1_interleaved && !iter_ended[idx] && !is_single_ended {
441 +                         iter.advance()
442 +                             .fastq_err(paths[idx].as_ref().unwrap(), (rec_num[idx] + 1) * 4)?;
443 +                         let record = iter.get();
444 + 
445 +                         // Check for non-ACGTN characters
446 +                         if let Some(ref rec) = record {
447 +                             if !fastq::Record::validate_dnan(rec) {
448 +                                 let msg = "FASTQ contains sequence base with character other than [ACGTN].".to_string();
449 +                                 let e = FastqError::format(
450 +                                     msg,
451 +                                     paths[idx].as_ref().unwrap(),
452 +                                     rec_num[idx] * 4,
453 +                                 );
454 +                                 return Err(e);
455 +                             }
456 + 
457 +                             if sample {
458 +                                 let which = WhichRead::read_types()[idx + 1];
459 +                                 let read_length = read_lengths[which as usize];
460 +                                 let tr = TrimRecord::new(rec, read_length);
461 +                                 rp.push_read(&tr, which)
462 +                             }
463 +                         } else {
464 +                             // We should only hit this if the FASTQ has an odd
465 +                             // number of records. Throw an error
466 +                             let msg = "Input FASTQ file was input as interleaved R1 and R2, but contains an odd number of records".to_string();
467 +                             let e = FastqError::format(
468 +                                 msg,
469 +                                 paths[idx].as_ref().unwrap(),
470 +                                 rec_num[idx] * 4,
471 +                             );
472 +                             return Err(e);
473 +                         }
474 + 
475 +                         rec_num[idx] += 1;
476 +                     }
    |
}
Expand Down Expand Up @@ -653,6 +642,7 @@ mod test_read_pair_iter {

let res: Result<Vec<ReadPair>, FastqError> = it.collect();
assert!(res.is_ok());
println!("{:#?}", &res);
assert_eq!(res.unwrap().len(), 8);
}

Expand Down

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