Issue 207 #8
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Issue 207 #8
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…t level of approximation kicks in *before* loading transcript data: that should speed things up as well.
…reation and checking to the subprocesses. This should speed it up a lot in the presence of complex, long loci.
…aximum length. This should prevent stray transcripts from botched prepare runs to take up too much time.
Codecov Report
@@ Coverage Diff @@
## master #8 +/- ##
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+ Coverage 79.54% 79.57% +0.02%
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Files 70 70
Lines 15589 15628 +39
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+ Hits 12401 12436 +35
- Misses 3188 3192 +4 |
lucventurini
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Feb 11, 2021
lucventurini
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Feb 11, 2021
This PR deals with the fact that Mikado pick was not leveraging correctly the multiple processors. This was due to the fact that the main process was taking up the job of checking transcripts and creating loci - expensive operations that acted as bottlenecks. Now the main process will only collate transcripts as GTF rows, do a minimal check on the fact that they do not have introns longer that the maximum size, and then and only then dispatch them. Moreover, the trigger to user reduction methods in a locus has been lowered (from 10,000 to 5,000) and the first method (removal of redundant, completely contained intron chains) will be triggered before loading transcript data from the database.
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General improvements in speed, especially for multiprocessing; also, now Mikado pick will check at runtime whether there are transcripts that have too big introns and remove them.