[feat] add an option to only process specific lanes #36
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nh13
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tfenne and
omicsorama
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tfenne and
omicsorama
nh13
commented
Jan 11, 2023
nh13
commented
Jan 11, 2023
| @@ -346,12 +360,12 @@ impl Opts { | |||
| Some(Ok(record)) => { | |||
| if first_head.is_empty() { | |||
| first_head = record.head().to_vec(); | |||
| end_index = first_head.find_byte(b' ').unwrap_or(first_head.len()); | |||
| end_index = first_head.find_byte(b':').unwrap_or(first_head.len()); | |||
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I think this was a bug, since the lane is in the read name prior to the first space.
nh13
commented
Jan 11, 2023
| assert!(result.is_err()); | ||
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|
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| // Path prefix | ||
| //Index FASTQ found and not extracting sample barcode from FASTQ header, | ||
| // so should be ok | ||
| let result = Opts::from(vec![prefix], vec![], false); | ||
| let result = Opts::from(&vec![prefix], &vec![], false, &vec![]); |
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I'd love to have defaults in rust
Only samples (in the sample sheet) and FASTQs (with known lane numbers) will be processed that match the provided list of lanes. This option cannot be used when the lane for a FASTQ is not known (e.g. when the FASTQS are explicitly given on the command line). Also allow the same sample_id/barcode combination is used across lanes for a given sample. Previously an error would occur, now the repeated sample is treated as one sample (just in many lanes). Other changes: - the read name is only checked up to the first colon within a group of FASTQS (e.g. R1 across lanes) - print out the # of threads being used
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omicsorama
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Jan 12, 2023
|
@tfenne I accidentally merged this, please still review, and then I can incorporate changes in a separate PR. |
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Only samples (in the sample sheet) and FASTQs (with known lane numbers) will be processed that match the provided list of lanes. This option cannot be used when the lane for a FASTQ is not known (e.g. when the FASTQS are explicitly given on the command line).
Also allow the same sample_id/barcode combination is used across lanes for a given sample. Previously an error would occur, now the repeated sample is treated as one sample (just in many lanes).
Other changes: