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Refactoring to use stream modules #7

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tiagofilipe12 opened this issue Jun 2, 2017 · 2 comments
Open

Refactoring to use stream modules #7

tiagofilipe12 opened this issue Jun 2, 2017 · 2 comments

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@tiagofilipe12
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@tiagofilipe12 tiagofilipe12 commented Jun 2, 2017

Refactor to use through2, split2, pumpify.

@tiagofilipe12 tiagofilipe12 self-assigned this Jun 2, 2017
@tiagofilipe12 tiagofilipe12 changed the title Refactoring Refactoring to use stream modules Jun 2, 2017
@bmpvieira bmpvieira added this to In Progress in Bionode Project Board Jun 2, 2017
@thejmazz
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@thejmazz thejmazz commented Jun 2, 2017

Also, something to consider, we can do object stream of like { name, seq, name2, quality }, or somehow do it in a way that lets the seq and quality themselves be streamed. Else you need to store the entire seq and quality in memory (in the object) which somewhat defeats the purpose of streaming.

@tiagofilipe12
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@tiagofilipe12 tiagofilipe12 commented Jun 2, 2017

I have made some changes to accomplish this but still experimental. Checkout branch Refactoring. Also, added a sample file with some possible problems while parsing fastq (check it here). Now, it handles empty lines, both with spaces and no spaces and can at the same time handle "@" character in quality recognizing properly the name. Please test it and see what you think (just run ./lib/bionode-fastq.js, since it has a test here).

@bmpvieira bmpvieira moved this from In Progress to Next in Bionode Project Board Aug 23, 2017
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