DRAFT: SortFastq #38
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DRAFT: SortFastq #38
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nh13
requested changes
Feb 13, 2025
| impl Command for SortFastq { | ||
| /// Executes the sort_fastq command | ||
| fn execute(&self) -> Result<()> { | ||
| let mut fq_reader = FastqReader::from_path(&self.input)?; |
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You probably want to use FastqReader::with_capacity(1024 * 1024) or something large like we do in the demux tool
| LimitedBufferBuilder, | ||
| > = ExternalSorterBuilder::new() | ||
| .with_tmp_dir(Path::new("./")) | ||
| .with_buffer(LimitedBufferBuilder::new(self.max_records, true)) |
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- any reason not to expose the tmp dir on the command line, and have it by default be
None(use the system default)? - I would think a big win for this tool would be to use
with_threads_number. Shall we use multiple threads? - I would also try to use
with_rw_buf_sizewith1024 * 1024
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Initial attempt at #3
Tested on an empty FASTQ as well as a ~10GB one. It seems to be working.
Looks like fgbio is consistently faster. Should look into why. Library/sorting algorithm/my usage?
Should add unit tests at minimum + any feedback if dev interest in merging.