Stories:
https://www.pivotaltracker.com/story/show/66263868
Bug:
The problem was due to the way we were calculating the fix penalty of a large deletion or insertion. In this case we calculate the alignment likelihood of the portion
or read or haplotype deletion as the penalty of that deletion/insertion without going through the full pair-hmm process. For large events this resulted in a 0 in
in linear scale computations that ins transformed into an infinity in log scale.
Changes:
- Change to use log10 scale for calculate those penalties.
- Minor addition of .gitignore to hide ./public/external-example/target which is generated by the building process.
-Acquire file locks in a background thread with a timeout of 30 seconds,
and throw a UserException if a lock acquisition call times out
* should solve the locking issue for most people provided they
RETRY failed farm jobs
* since we use NON-BLOCKING lock acquisition calls, any call that
takes longer than a second or two indicates a problem with the
underlying OS file lock support
* use daemon threads so that stuck lock acquisition tasks don't
prevent the JVM from exiting
-Disable both auto-index creation and file locking for integration tests
via a hidden GATK argument --disable_auto_index_creation_and_locking_when_reading_rods
* argument not safe for general use, since it allows reading from
an index file without first acquiring a lock
* this is fine for the test suite, since all index files already
exist for test files (or if they don't, they should!)
-Added missing indices for files in private/testdata
-Had to delete most of RMDTrackBuilderUnitTest, since it mostly tested auto-index
creation, which we can't test with locking disabled, but I replaced the deleted
tests with some tests of my own.
-Unit test for FSLockWithShared to test the timeout feature
- Fixed shell glob limitation that was failing license updates on big commits
- Hook will now force user to re-commit after updating the licenses (pre-commit hook can't update and commit in the same process)
- Moved all scripts to bash/zsh
- Separated the license utilities in a separate python module to avoid copying code
GSATDG-28 #resolve
Geraldine Van der Auwera
Valentin Ruano-Rubio
Khalid Shakir
Joel Thibault
David Roazen
Mauricio Carneiro
Mark DePristo