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v2.4.2
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@mirimia mirimia released this 29 May 09:48
· 116 commits to master since this release
v2.4.2
469bff5

Improvements in speed and performance.

Improvements

  • A batch of improvements has been implemented in combine to increase computing speed. First, combine can take up to 6 cores to parallelize the generation of inclusion tables. Second, the quantification of pseudo-PSIs for ALTA and ALTD events (added in version v2.2.1, and used for the --min_ALT_use option) has been simplified to reduce computing time. It currently uses more local quantification, as the ANN module. PSIs of individual alternative splice sites do not change. Finally, a few complex events were removed.

  • align includes a sanity check when paired reads are provided and it will die if the number of R1 and R2 reads are different.

  • It is now possible to provide group names in compare (otherwise, they will still be automatically generated from the first replicate name).

Updates and fixes

  • Silent change in align to use a more efficient hash system to store counts by position. This has seemingly given issues to a user with hg38.
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