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lh3 / miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)
MIT License
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sam2paf javascript code #15

Closed cjain7 closed 8 years ago

cjain7 commented 8 years ago

Hi,

I am trying to run the sam2paf javascript code to do the format conversion. Due to no prior experience with javascript, I have been following multiple ways, mentioned online to get the code running on mac/linux, but saw no success so far. Do you have the conversion script written in other language? or can you supply some tips on how to compile/execute this file?

On mac, I tried the following:

/System/Library/Frameworks/JavaScriptCore.framework/Versions/Current/Resources/jsc miniasm/misc/sam2paf.js bwa.30K.sam

Exception: ReferenceError: Can't find variable: File global code@miniasm/misc/sam2paf.js:1:63 Could not open file: bwa.30K.sam

lh3 commented 8 years ago

Well, that script is not intended for end users. If you want to try anyway, download k8 precompiled binary here and run the script with:

k8-linux sam2paf.js <in.sam>

Let me know if that works.

PS: there is a mac binary in the k8 package as well.

cjain7 commented 8 years ago

Works, thanks.