Updated COSMIC to annotate protein change strings with their counts. #5181
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LeeTL1220
reviewed
Sep 13, 2018
| final String proteinChange = getProteinChangeStringFromResults(resultSet); | ||
| if ( !proteinChange.isEmpty() ) { | ||
| if ( proteinChangeCounts.containsKey(proteinChange) ) { | ||
| proteinChangeCounts.put(proteinChange, proteinChangeCounts.get(proteinChange) + 1); |
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There is a better method to use to do this:
final int count = proteinChangeCounts.getOrDefault(proteinChange, 0);
proteinChangeCounts.put(proteinChange, count+1);
| } | ||
| catch (final SQLException ex) { | ||
| throw new GATKException("Cannot get Protein Position from column: " + GENOME_POSITION_COLUMN_NAME, ex); | ||
| throw new GATKException("Cannot get Protein Change from column: " + GENOME_POSITION_COLUMN_NAME, ex); |
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I think protein change should be lower case
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Now the COSMIC data source produces counts of each protein change found in the COSMIC database.
That is, rather than a raw count of the total number of protein changes (e.g.
2or7), it produces a count of each specific protein change found in the COSMIC database that overlaps a variant (e.g.p.E545K(2)orp.E545K(2)|p.E542K(2)|p.H1047R(2)|p.N345K(1)).Fixes #4400