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setting "--format fastq" with gzip-compressed FASTQ crashes falco #43

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guilhermesena1 opened this issue Sep 23, 2022 · 0 comments
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setting "--format fastq" with gzip-compressed FASTQ crashes falco #43

guilhermesena1 opened this issue Sep 23, 2022 · 0 comments
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@guilhermesena1
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and this is because it is reading the gzip-compressed FASTQ as if it was a normal FASTQ file. I'm not 100% sure but I believe FastQC runs normally when this set of parameters is used, so falco must behave similarly.

We can probably be able to figure out if it's compressed or not prior to processing, probably use igzfstream from smithlab_cpp would be the best option.
@guilhermesena1 guilhermesena1 added the bug Something isn't working label Sep 23, 2022
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