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ksahlin / strobealign

Aligns short reads using dynamic seed size with strobemers
MIT License
128 stars 16 forks source link

Fix invalid QUAL for FASTA input #288

Closed marcelm closed 1 year ago

marcelm commented 1 year ago

The QUAL field needs to be set to * for missing qualities, but we just wrote record.qual directly, which is empty for FASTA input.

Because there’s no way to distinguish empty FASTQ records from empty FASTA records in kseq++, this changes output slightly: For empty FASTQ records, the QUAL fiel is now set to * instead of the empty string. This should not matter in practice.

Closes #287

ksahlin commented 1 year ago

Great!

marcelm commented 1 year ago

Should we make a new release? A couple of fixes have been sitting in main for two months, would be good to get them out to the users.

ksahlin commented 1 year ago

Sure, but New bucket index vector not merged in and included? Sent from my iPhoneOn 5 Jun 2023, at 09:40, Marcel Martin @.***> wrote: Should we make a new release? A couple of fixes have been sitting in main for two months, would be good to get them out to the users.

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