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@ksahlin ksahlin released this 02 Feb 23:47
0.2.5.1
d4567f3

Stable version before major re-write of code resulting in improved readability and significant speedup in statistical test. This release fixed several minor bugs present in the IsoCon version (commit 85eb122, tag 0.2.4) that was used to generate results in the bioRxiv preprint made available 2018-01-10, as well as the version sent to a journal for review.

Fixed

  • Bugfix in if-statement described in Supplementary Section A: "Estimating the probability of a sequencing error" biorxiv-suppl.
  • Bugfix in how to treat tiebreakers, described in Supplementary Section A: "implementation details" in
    biorxiv-suppl.

Added

  • Test data and instructions for running IsoCon on testdata.
  • Automatic builds and testing with Travis.
  • Installation through pip now possible.
  • Parameter --verbose and also removed lot of prints to stdout.
  • Added parameter --min_exon_diff to break alignment with this many consecutive '-' (an indel). Previously this was hardcoded.
  • Made the mapping quality values upper bound T (described in Supplementary Section A: "Estimating the probability of a sequencing error"biorxiv-suppl) a parameter --max_phred_q_trusted instead of hardcoded value.

Changed

  • change parameter --single_core (a flag that was false by default and IsoCon would use all cores available) to a more flexible format --nr_cores where the used can specify how many cores.
  • Changed terminology. All occurences of "minimizer" is changed to "nearest_neighbor" (or "neighbor" in parameters) to adapt for new notation of nearest neighbor graph instead of minimizer graph.

Removed

  • Removed option --barcodes as it serves no purpose anymore --- if we have barcodes they have been detected and reads have been split into batches in a upstream step.
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