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timbitz / Whippet.jl

Lightweight and Fast; RNA-seq quantification at the event-level
MIT License
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curseq is GTCTTGTTGTTGGGCTTG of type BioSequences.BioSequence{BioSequences.DNAAlphabet{2}} #110

Closed rfara closed 3 years ago

rfara commented 3 years ago

Problem:

The line of code:

println("curseq is ", curseq, " of type ", typeof(curseq))

seems to print every seed sequence in the terminal:

curseq is GTCTTGTTGTTGGGCTTG of type BioSequences.BioSequence{BioSequences.DNAAlphabet{2}}

When I run a whippet-quant job on my cluster, the logfile becomes absolutely enormous. Maybe this also slows things down - I have no idea.

Solution:

Comment out/remove line 170 of src/align.jl.

I fixed the issue for myself by just commenting the line out. Maybe this will have some catastrophic issue. If so, please let me know!

timbitz commented 3 years ago

@rfara thanks for reporting-- looks like a debugging line left over from @gmassman, commenting out is correct. I'll also look into #111, and push fixes for the v1.5 release.

timbitz commented 3 years ago

Fixed in master as of #113