| ▲ | totalperspectiv a day ago |
| Removing the wrapping newline from the FASTA/FASTQ convention also dramatically improves parsing perf when you don't have to do as much lookahead to find record ends. |
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| ▲ | Gethsemane a day ago | parent | next [-] |
| Unfortunately, when you write a program that doesn't wrap output FASTAs, you have a bunch of people telling you off because SOME programs (cough bioperl cough) have hard limits on line length :) |
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| ▲ | sharedptr 11 hours ago | parent | next [-] | | Is BioPerl still standard, did people move to BioPython? When I was shown BioPerl I was tempted to write a better, C++ version, but was overwhelmed by other university stuff and let it go. | |
| ▲ | o11c a day ago | parent | prev [-] | | You can use content-defined chunking to wrap at a predictable place so that compression still works. |
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| ▲ | bede a day ago | parent | prev [-] |
| Thanks for reminding me to benchmark this! |
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| ▲ | totalperspectiv a day ago | parent [-] | | I've only tested this when writing my own parser where I could skip the record end checks, so idk if this improves perf on a existing parser. Excited to see what you find! |
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