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molgenis / gavin-plus

A platform for standardized modular downstream genome analysis.
GNU Lesser General Public License v3.0
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Fix #65: Option to not print prefix for RLV fields and possibly 64: variants out of order #66

Closed bartcharbon closed 6 years ago

molgenis-jenkins commented 6 years ago

SonarQube analysis reported 78 issues

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Top 10 extra issues

Note: The following issues were found on lines that were not modified in the pull request. Because these issues can't be reported as line comments, they are summarized here:

  1. CRITICAL Main.java#L130: Refactor this method to reduce its Cognitive Complexity from 44 to the 15 allowed. rule
  2. CRITICAL AssignCompoundHet.java#L31: Refactor this method to reduce its Cognitive Complexity from 67 to the 15 allowed. rule
  3. CRITICAL PhasingCompoundCheck.java#L58: Refactor this method to reduce its Cognitive Complexity from 64 to the 15 allowed. rule
  4. CRITICAL TrioFilter.java#L77: Refactor this method to reduce its Cognitive Complexity from 160 to the 15 allowed. rule
  5. CRITICAL TrioFilter.java#L165: Define a constant instead of duplicating this literal "REFERENCE" 8 times. rule
  6. MAJOR Main.java#L96: Replace this use of System.out or System.err by a logger. rule
  7. MAJOR Main.java#L125: Replace this use of System.out or System.err by a logger. rule
  8. MAJOR Main.java#L127: Replace this use of System.out or System.err by a logger. rule
  9. MAJOR Main.java#L141: Replace this use of System.out or System.err by a logger. rule
  10. MAJOR Main.java#L147: Replace this use of System.out or System.err by a logger. rule