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Fastq format bugfix #46

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Psirving wants to merge 2 commits into master from fastq_format_bugfix

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Psirving commented Jul 14, 2023

2 bug fixes:

'+' entry of fastq files were not allowed to have content, despite being valid fastq format, and ShapeMapper2 not caring about this content. Very annoying for SRA file downloads.
--amplicon and --correct-seq used simultaneously produced an error because MutationCounter, MutationParser, and SequenceCorrector components were not given names or associated RNA targets. See issue not understandable Error message about primers #31.

Tony or Lucas, can you double check these? We have been using them in Shapemapper 2.1.5 with no issues yet, but untested with 2.2.0.

Psirving added 2 commits

July 13, 2023 22:43


          content after '+' is a valid fastq file

c028761


          multiple fasta + sequence correction require name and assoc_rna args

3ca4453

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