update cosmic importer for new cosmic datafiles

[MatthijsPon]

Update Cosmic data importer to parse Legacy ID and recognise new HGSVp nomenclature

ImportCosmicData.java
COSV identifiers do not map to the COSMIC webpage correctly, COSM identifiers are still present in INFO string, take these as COSMIC IDs.

MutationKeywordUtils.java
Line 153 - Frameshift was not recognised when starting at stop codon.
Line 169 - Add other silent mutation options
Line 184 - Insertion just before stop codon not recognised (A101_*102insAA)
Line 189-194 - New HGSVp keyword ext, implemented as insertion
Line 196-200 - New HGSVp keyword dup, implemented as insertion
Line 226 - New HGSVp keyword delins, added to existing delins-like structure

• Line 230 - Edited matching group to reflect new changes at line 226
  Line 242-246 - New HGSVp keyword delins with 1 del and >1 ins, not captured by an earlier regex
  Line 248-261 - New HGSVp keyword delext implemented in a similar structure as delins, excluding n1 > n2 option, as this would not be a delext

TestMutationKeywordUtils.java
Added tests for new implementations.

Checks

• Has tests or has a separate issue that describes the types of test that should be created. If no test is included it should explicitly be mentioned in the PR why there is no test.
• The commit log is comprehensible. It follows 7 rules of great commit messages. For most PRs a single commit should suffice, in some cases multiple topical commits can be useful. During review it is ok to see tiny commits (e.g. Fix reviewer comments), but right before the code gets merged to master or rc branch, any such commits should be squashed since they are useless to the other developers. Definitely avoid merge commits, use rebase instead.

[sonarcloud]

SonarCloud Quality Gate failed.   

0 Bugs
0 Vulnerabilities
1 Security Hotspot
16 Code Smells

0.0% Coverage
16.0% Duplication

[pvannierop]

Thanks!