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Releases: bcgsc/ntJoin

ntJoin v1.1.5

19 Aug 20:30
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  • Release version 1.1.5
  • Fix for cases where no scaffolding was seen for circular references (#113)
    • With fix, circular graphs are detected and properly used for scaffolding sequences
  • Documentation update - ensure that any terminal N's in sequences are removed prior to ntJoin

ntJoin v1.1.4

05 Feb 19:58
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  • Release version v1.1.4
  • Large code refactor
  • Bugfixes

ntJoin v1.1.3

12 Sep 20:52
428527c
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  • Release version v1.1.3
  • Bugfix for edge case
    • Where there are no paths found and overlap=True

ntJoin v1.1.2

08 Sep 16:08
5c31a9a
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  • Release version v1.1.2
  • Fix for compatibility with new pybedtools version (v0.9.1+)
  • Code refactoring
  • Documentation updates

ntJoin v1.1.1

25 Jul 16:51
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  • Release version v1.1.1
  • Make btllib a dependency (removed packaged btllib)
  • Documentation updates

ntJoin v1.1.0

30 May 22:57
a62b241
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  • Release version v1.1.0
  • Introduces new 'overlap' feature, which is enabled by default (overlap=True)
    • For adjacent sequences that have a putative overlap based on gap distance estimates:
      • Compute minimizers with a lower k and w (to increase sensitivity), and create an undirected minimizer graph using minimizers found in the putative overlap region (in multiplicity of 1 in both sequences)
      • Use the minimizer graph to anchor the sequences to each other, and use the coordinates to trim the overlapping sequence
    • This feature reduces the incidence of local misassemblies and duplications, created when overlapping sequences are naively joined end-to-end
  • Update btllib to v1.4.4
  • General bugfixes and documentation updates

ntJoin v1.0.8

06 Oct 22:47
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  • Release version v1.0.8
  • Add support for multi-line fasta files
  • Update btllib dependency to v1.1.5

ntJoin v1.0.7

23 Jun 00:18
ef2276d
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  • Release version v1.0.7
  • Update btllib dependency (to v1.1.2)
  • Bugfixes

ntJoin v1.0.6

05 Feb 19:19
e5b8437
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  • Release version v1.0.6
  • Added optional parameter reference_config, which can be used to specify a config file that lists the reference(s) and reference_weight(s)
    • Previous ntJoin usage will work in exactly the same way if this parameter is not used - this feature is just provided for convenience, particularly for specifying multiple references
    • Config file expected to be in csv format in the form:
reference_1.fa,reference_weight_1
reference_2.fa,reference_weight_2

ntJoin v1.0.5

20 Nov 17:56
1104d52
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  • Release version v1.0.5
  • Fixes for indexlr