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v4.rst

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v4.0.1

  • Update GeUtilities version to its current latest where the issue of duplicate regions is resolved. #123

v4.0

MSPC v4 is a major overhaul of performance, user-experience, and change CLI assembly name to mspc. This version also adds scripts to validate MSPC's output.

-Performance
  • 24x faster performance (see PR # 78);
  • 59% less memory footprint (see PR # 75 and 77);
-User-experience
 
  • More arguments;
  • Better logging;
  • Export results in standard BED and txt format with more information.

Remarks

  • Performance
    • Improve processing Supporting peaks [PR # 78];
    • Collapse multiple interval trees into a single tree [PR # 77];
    • Memory optimization by improving how attributes are stored for a processed peak [PR # 75];
    • Build a tree after all intervals are added (at "Initializing" step), not at first time the tree is queried [PR # 71];
    • Make tracking a list of overlapping peaks an optional feature, which is disabled by default [PR # 74];
  • User-experience
    • Adds the option of specifying degree of parallelism [PR # 89];
    • Add an option to specify the output path [PR # 73];
    • Export data in both standard BED and MSPC format that in addition to info in BED it contains X-sqrd, right-tail probability, and adjusted p-value [PR # 69];
    • Parser and export double types appreciating culture info [PR # 101];
    • Fix a bug truncating column content [PR # 83];
    • Raise an exception when a given parser config file does not exist [PR # 90];
    • Formatting and colouring error and success messages [PR # 91];
    • Log input filename differently for Logger and Console [PR # 92];
    • Add - and -- before missing argument names [PR # 94];
    • Add the option to specify a folder where to read input files [PR # 95];
    • Report CLI table headers in log file [PR # 103];
    • Report elapsed time in the output [PR # 106];
    • Update documentation and README [PR # 107];
    • Hint how to use help when an exception occurs [PR # 108]
    • Update installation documentation [PR # 110]
  • Architecture
    • Update target framework to .NET Core 3.0 [PR # 100];
    • Overhaul logging and orchestration [PR # 72];
    • Drop SonarScanner preview mode [PR # 84];
    • Drop SonarCloud integration [PR # 98];
    • Format appveyor and travis yaml files [PR # 99];
    • Change project logo [PR # 105];
    • Change CLI assembly name from CLI to mspc [PR # 109]