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Correct the expansion of UTR/CDSs in the padding #129

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lucventurini opened this issue Oct 2, 2018 · 2 comments
Closed

Correct the expansion of UTR/CDSs in the padding #129

lucventurini opened this issue Oct 2, 2018 · 2 comments
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@gemygk @lucventurini
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bug enhancement
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2.0

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@lucventurini
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At the moment, the expansion does not happen correctly. Namely, the CDS ends up always being one base off and therefore gets thrown away.

This issue will track improvements on this front.
lucventurini added a commit that referenced this issue Oct 2, 2018
@lucventurini
Tentative improvements for #129
2a0b5d2
lucventurini added a commit that referenced this issue Oct 2, 2018
@lucventurini
Hopefully corrected for the offset - issue #129
7a4a075
@lucventurini
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Region 0:6541786-6575880 is another candidate for testing this problem, this time on the negative strand. Initial testing with the current version in the branch yielded incorrect results, while the tests on the positive strand passed. This indicates that probably something is amiss in the reverse complement.

lucventurini added a commit that referenced this issue Oct 3, 2018
@lucventurini
This bug fix and associated test should finally close #129. Tomorrow …
b76b734 
…more testing.
lucventurini added a commit that referenced this issue Oct 3, 2018
@lucventurini
Fixed the bug found by @gemygk in the last run (still pertaining to #129
9794cbc 
)
@lucventurini lucventurini added this to the 1.3 milestone Oct 5, 2018
@lucventurini
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Closing for now as no related bugs have been reported for now.

lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Tentative improvements for EI-CoreBioinformatics#129
df907df
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Hopefully corrected for the offset - issue EI-CoreBioinformatics#129
5191c28
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
This bug fix and associated test should finally close EI-CoreBioinfor…
72445b1 
…matics#129. Tomorrow more testing.
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Fixed the bug found by @gemygk in the last run (still pertaining to E…
6e1117b 
…I-CoreBioinformatics#129)
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@lucventurini lucventurini

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@gemygk @lucventurini