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Number of reads in fastq files not detected correctly. #112
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Hello, This would only be a problem in the fastq is compressed but has not .gz at the end, right? M |
I was getting this error when using uncompressed fastqs as input. I never tried the case of a compressed fastq without the |
I see. I'll add your fix for uncompressed reads (which I have never used as input). |
I mean try it first, not sure my perl code is that good ;) I sometimes use uncompressed fastqs as it saves time when processing fastqs from |
I'm having the same error with uncompressed files. The output of |
Sorry, my bad, I never dealt with this, as we never used uncompressed reads. I have implemented your solution, Joao, and committed the change. Could you please test it? For compressed reads, it works already (we ran it a billion times). |
Hi Manu,
If doing
wc -l file.fastq
you get12456 /path/to/file.fastq
but if doingwc -l file.fastq.gz
you get12345
.This gives an error that doesn't break
vast-tool align
that looks like this:The code below shows the problem.
I think a simple fix would be to pipe the
wc -l
into agrep
and add an if statement to check that$N_fq1
and$N_fq2
are numbers.but double check to make sure that's right.
Nicco
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