Ward D comments

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                                            Ward D

AttributeError: 'list' object has no attribute 'name'

This indeed is a bug in the error reporting, but the underlying problem is that there are no common chromosomes in file1.bam and file2.bam, you should double check that..

add plotPCA test

> I have a general question, would it be good to have those tests added to the current deeptools version as well. So that we can compare results? Yea, that's...

Typo/Bug in heatmapper.py script

Thanks for the report, this is taken up with #1325, and will be released soon.

computeMatrix runs substantially slower than expected

Thanks for the detailed report. We're aware computeMatrix (and others) scale rather poorly with respect to the number of regions (or number of samples, for that matter). We're working on...

computeMatrix scale-regions A region that is shorter than the bin size

note that computeMatrix also has a binSize argument to, which defaults to 10. in your case, the 'region shorter then the binsize, after accounting for unscaled regions' refers to: length...