Share project "gps-variant-parser" into "https://code.oicr.on.ca/svn/ferrettilab"
Share project "gps-variant-parser" into "https://code.oicr.on.ca/svn/ferrettilab"
Minor tweaks to the domain interface - necessary to integrate with Grails
Added initial HotSpot parser - handles the sample data sent by Andrew. Note that this even permits the .xslx files to work fine
Updated pom.xml and svn:ignore for proper Eclipse integration clunkish nonsense
Added a bunch of source cleanups and configuration fixes, which mean we almost have no warnings now apart from a few funny enum cast hacks deep in the parsing code
Updated parsing to suppress warnings at the critical point that remains.
Updated teh pomz with all requisite project stuff, and its now set up on Jenkins, so we can start to integrate
Updated to create a RunAssay, not linked to an Assay, for the HotSpot parser. This is necessary to provide the panel associations. pom cleaned up a bit more
This is an immense commit, but contains most of the changes needed to reconfigure to a precise notion of a mutation. The parser is split out as a separate Maven-built component, and the Perl code used to calculate positions against hg19 is now ported to Java, along wth refGene.txt, and embedded in the parsing component. This completes the Sanger mutation handling. The knowledge base now uses an XML representation, and is loaded with COSMIC data separately - both are dramatically more detailed. There is some debugging and testing to do yet.
Make sure we load from the parsers's jar, rather than from the ClassLoader. This is necessary for the parser to work after integration
Modified Sanger test file to reflect GPS-112
Now removes spaces from mutations in Sanger, before locating. GPS-112
Updated version in pom
Various corrections to the gps-variant-parser
Removed unused code and suppressed various warnins where leaving the code made more sense for future use.
Updated to 0.0.2-RELEASE, by including a system for identifying the strand direction for a given NCBI identifier. This isn't actually used yet, but it will need to be some time, when we are properly managing the COSMIC merge to normalize for strand direction. We also have a direction compensator class that can be used independently to flip codes for a strand direction. This is used.
Moved test file to right place (otherwise shouldn't compile!) and updated pom.xml to be more specific on JUnit versioning
Corrected the Sequenom parsing, which assumed that the panel was always called OncoCarta. This now uses similar logic to PacBio/HotSpot, and parses the panel name and version from the row for the process. This is then used in the target lookup.
Updated version