fixes, closes #121 #122 #126 #127

[CLAassistant]

All committers have signed the CLA.

[tomazc]

@JureZmrzlikar please sign the CLA.

[tomazc]

@JureZmrzlikar, please check and fix the linters issue in travis.

[codecov-io]

Codecov Report

Merging #129 into master will increase coverage by -0.1%.

@@            Coverage Diff            @@
##           master     #129     +/-   ##
=========================================
- Coverage   82.49%   82.39%   -0.1%     
=========================================
  Files          50       50             
  Lines        3210     3209      -1     
=========================================
- Hits         2648     2644      -4     
- Misses        562      565      +3

Impacted Files	Coverage Δ
iCount/tests/test_peaks.py	98.18% <ø> (ø)	:white_check_mark:
iCount/tests/test_externals.py	98.14% <ø> (-0.27%)	:x:
iCount/externals/cutadapt.py	87.5% <ø> (-12.5%)	:x:
iCount/externals/star.py	87.23% <ø> (-2.13%)	:x:
iCount/files/fastq.py	64.76% <100%> (ø)	:white_check_mark:
iCount/analysis/clusters.py	100% <100%> (ø)	:white_check_mark:
iCount/tests/test_ensembl.py	97.7% <100%> (+0.11%)	:white_check_mark:
iCount/genomes/ensembl.py	92.54% <100%> (+1.35%)	:white_check_mark:
iCount/analysis/peaks.py	94.66% <66.66%> (-0.61%)	:x:

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[JureZmrzlikar]

@tomazc : commit 3c66679 does indeed fix the repeated columns issue. The problem was that input variable with filename was overridden with the contents of the file. While logging the inputs, whole content of the file was logged. At that stage file is not merged yet, so output appeared as it was the result.

[JureZmrzlikar]

@tomazc : all tests pass, except coverage. Do you insist on making a positive diff, or is it OK? I removed some tests, since they were failing for some strange mocking reasons... I personally don't think it is worth bothering, but my opinion may be biased :-)

[tomazc]

@JureZmrzlikar, great, thanks!