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@timothymillar timothymillar released this 15 Jul 22:15
· 35 commits to master since this release
v0.3.0
15b49b6
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Learn about vigilant mode.
  • new features
    • informative reads
      • option to include soft-clipped tips in place of their mate informative read
      • option to exclude full-length informative reads completely
    • output formats
      • outputs with the .gz extension are compressed with block-gzip rather than regular gzip #104
      • option to output tab-delimited plain text files suitable for tabix indexing when block-gzipped #103
    • extract-informative temporary files #106
      • temporary files are now written to the same location as the output by default
      • option to not remove these files
      • option to write them to a temp location provided by the operating system
  • changes
    • added Biopython as a dependency to support block-gzip compression
    • refactor submodules to hide application specific code
    • refactor clustering classes/methods to use new names
      • non-hierarchical method named IDBCAN (Interval Density Based Clustering of Applications with Noise)
      • conservative-hierarchical method named SIDBCAN (Splitting-IDBCAN)
      • aggressive-hierarchical method named SIDBCAN-aggressive and deprecated
  • bug fixes
    • python 3 shebang lines #98
    • add MANIFEST.in to allow for github install with pip #89
  • documentation
    • named clustering algorithms loosely based on DBSCAN
      • non-hierarchical method named IDBCAN (Interval Density Based Clustering of Applications with Noise)
      • hierarchical method named SIDBCAN (Splitting-IDBCAN)
    • many corrections to documentation of clustering algorithms #99
    • specify tabix command to index block-gzipped output
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