NullPointerException when starting ASCAT jobs

[Nicklas Nordborg]

This is the stacktrace:

java.lang.NullPointerException: Cannot invoke "net.sf.basedb.core.File.getName()" because "normalBam" is null
        at net.sf.basedb.reggie.grid.AscatJobCreator.createAscatJobs(AscatJobCreator.java:257)
        at net.sf.basedb.reggie.servlet.AscatServlet.doPost(AscatServlet.java:411)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:528)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:596)

When checking the list of items that are displayed in the "Start ASCAT" wizard it seems like tumor alignments are matched against normal alignments that are still waiting in the job queue for being aligned. The error will go away once all alignments have been completed, but the code should of course be updated so that only completed alignments are selected.

There is probably a similar problem in the "Start variant calling" wizard.

[Nicklas Nordborg]

In 7765:

References #1599: NullPointerException when starting ASCAT jobs

Fixed for the ASCAT wizard.

[Nicklas Nordborg]

In 7766:

Fixes #1599: NullPointerException when starting ASCAT jobs

Fixed for the Variant calling wizard.