Issues with Int8Handler

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Issue #4 resolved
Stefan created an issue


I came back to some mappability analyses I did with umap some time ago and I still had my uint8 files. The mappability analysis I did was with two k-mer lengths: 100 and 150. When trying to run Int8Handler I got the error:

IOError: [Errno 2] No such file or directory: 'pathtofolder/kmers/k100/chr-1.uint8.unique.gz'

Which made sense given that my files are named <chrom>.<kmer>.uint8.unique.gz. In lines 25-27 of the Int8Handler code there's written:

The Int8Handler class requires in_dir argument which
is a directory with subfolders named as k<integer>
that have <chrom>.<kmer>.uint8.unique.gz files.

So up until here it corresponds to what I have, but then the parameter in_dir is described in line 32 as:

param in_dir: Directory with <chrom>.uint8.unique.gz files

There's some inconsistency here that needs to be addressed. In my case, to solve the issue I needed to change the Int8Handler code at line 95 for it to work.

Comments (3)

  1. Mehran Karimzadeh

    Hi Stefan,

    Thanks for reporting the issue. The Int8Handler requires the directory named as globalmap_k100tok150 in your case. Therefore you are right, the in_dir definition in the docstring is wrong.

    I will clarify that in the next release.

    Thanks again for reporting this.

    Best, Mehran

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