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Prevent loci from being lost due to chaining #131

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lucventurini opened this issue Oct 4, 2018 · 1 comment
Closed

Prevent loci from being lost due to chaining #131

lucventurini opened this issue Oct 4, 2018 · 1 comment
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@gemygk @lucventurini
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Version 2
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2.0

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@lucventurini
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Currently, due to the architecture of Mikado, it can happen that loci get lost in scenarios like the following:

  • Real loci to find: transcript A, transcript B
  • Transcript C spans both loci and shares an intron with A but not with B. C is not a valid alternative splicing event for B.
  • Sublocus stage: C wins over A, B wins as singleton
  • Monosublocus stage: B wins over C
  • Locus stage: We only have B as transcript, as C is discarded.
  • A is lost because no transcript has been retained for that locus.

This tends not to happen too much due to the specifics of scoring, but it is an issue.
Ideally, Mikado should realise it has lost transcripts, backtrack, and rebuild loci for them.
lucventurini added a commit that referenced this issue Oct 4, 2018
@lucventurini
Now superloci keep track of missed transcripts - first step for solving
655e634 
#131
lucventurini added a commit that referenced this issue Oct 4, 2018
@lucventurini
Narrowing down #131 and starting to implement the relevant tests
1024df5
lucventurini added a commit that referenced this issue Oct 4, 2018
@lucventurini
Implemented the unit-test that we have to beat for #131
36e3ac3
lucventurini added a commit that referenced this issue Oct 4, 2018
@lucventurini
We should have fixed #131
ffbff8b
@lucventurini lucventurini added this to the 1.3 milestone Oct 5, 2018
lucventurini added a commit that referenced this issue Oct 5, 2018
@lucventurini
Improvement on #131: now we are using a graph-based function, rather …
a94578e 
…than a for cycle, to find the missing loci. This also ensures coherence in terms of the overlapping parameters.
@lucventurini
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Correctly implemented. Closing.

@lucventurini lucventurini added this to Closed in Version 2 Oct 15, 2020
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Now superloci keep track of missed transcripts - first step for solving
0386e84 
EI-CoreBioinformatics#131
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Narrowing down EI-CoreBioinformatics#131 and starting to implement th…
049518b 
…e relevant tests
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Implemented the unit-test that we have to beat for EI-CoreBioinformat…
5bd57bc 
…ics#131
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
We should have fixed EI-CoreBioinformatics#131
2aa7c6d
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Improvement on EI-CoreBioinformatics#131: now we are using a graph-ba…
81b550e 
…sed function, rather than a for cycle, to find the missing loci. This also ensures coherence in terms of the overlapping parameters.
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