Sergey Venev

`cooler balance` is trying to ensure convergence of balancing algorithm by filtering out (ignoring) "misbehaving" bins: misbehaving bins are ones that have some sort of coverage "issues" - (1) too...

On a related topic - is it even possible to quickly check if a given `.cool` is balanced at all or not, via CLI? `cooler info` does not show it...

I'll leave it here, just in case: `h5dump -n filename.cool` yields HDF5 file content, e.g.: ``` HDF5 "blahblah_hg19.10000.cool" { FILE_CONTENTS { group / group /bins dataset /bins/chrom dataset /bins/end dataset...

oh my! that's handy! - I wish I read docs more carefully. But this one would only look for `weight` column in `bins`, right? It would return `False` in case...

@mimakaev there is no such well defined `mkl` interface as far as I understand - check screenshot - I have that `mkl` thing for sure, also conda/anaconda python installation: ![screenshot...

1. Just some relevant links here: https://docs.anaconda.com/mkl-service/ https://docs.anaconda.com/mkl-optimizations/ https://scicomp.stackexchange.com/questions/8193/how-to-tell-which-sequential-or-parallel-version-of-intel-mkl-is-linked 2. on a couple of linux system that I checked (ubuntu, rhel), `os.name` yields `posix`, not `linux`. I don't have a...

just posting a complete working example here : ```python from cooler.create import ArrayLoader import h5py import cooler h = h5py.File("cworld-test_hg19_C-40000-raw.hdf5", 'r') heatmap = h['interactions'] # create some bins , using...

it happens here: ``` process chunk_fastqs { tag "library:${library} run:${run}" storeDir getIntermediateDir('fastq_chunks') input: set val(library), val(run),file(fastq1), file(fastq2) from LIB_RUN_FASTQS_FOR_CHUNK output: set library, run, "${library}.${run}.*.1.fastq.gz", "${library}.${run}.*.2.fastq.gz" into LIB_RUN_FASTQ_CHUNKED script: chunksize_lines =...

it's actually a bug - @golobor add a label - to stick attention

@golobor it was someone in the lab, or elsewhere (maybe even myself) who tried to feed uncompressed fastq-s into distiller - and error or behaviour seems rather cryptic at that...