* Turn off the post-downsampler by default until new implementation.
* optimized read clipping in consensus regions -- only clip once instead of every time the window slides.
* extracted HeaderElement into it's own class.
* moved RFA to archive
* unified the context size of indels and mismatches
Cuts major corners for speed. Tests start in SECONDS instead of minutes.
SIGNIFICANT limitations (see below!)
Usage: ant fasttest -Dsingle=TestClass
The idea is that you do a regular "ant test -Dsingle=TestClass" (or "ant committests")
FIRST, then do "ant fasttest -Dsingle=TestClass" for all subsequent runs until
satisfied.
LIMITATIONS:
-REQUIRES that a full test build has already been done (using one of the
test targets like committests, or a manual "ant test.compile").
-Java only
-Single test class only
-No contracts
-Build jars in dist/ not updated, only classes in build/
-Version number output at runtime may be incorrect
-Classpaths to test the release jars were being constructed prematurely,
before all needed properties had been defined
-Added reportng as a TestNG dependency for testing purposes
* Targets to package and release lite/protected versions of the GATK/Queue
* Still TODO: -determine the actual directories where the protected releases should go
-update the Bamboo release plan
-fix a bug in the binary release test targets
Instead of creating a supposed network temporary directory locally which then fails when remote nodes try to access the non-existant dir, now checking to see if they network directory is available and throwing a SkipException to bypass the test when it cannot be run.
TODO: Throw similar SkipExceptions when fastas are not available. Right now instead of skipping the test or failing fast the REQUIRE_NETWORK_CONNECTION=false means that the errors popup later when the networked fastas aren't found.
- Merged Roger's metrics with Mauricio's optimizations
- Added Stats for DiagnoseTargets
- now has functions to find the median depth, and upper/lower quartile
- the REF_N callable status is implemented
- The walker now runs efficiently
- Diagnose Targets accepts overlapping intervals
- Diagnose Targets now checks for bad mates
- The read mates are checked in a memory efficient manner
- The statistics thresholds have been consolidated and moved outside of the statistics classes and into the walker.
- Fixed some bugs
- Removed rod binding
Added more Unit tests
- Test callable statuses on the locus level
- Test bad mates
- Changed NO_COVERAGE -> COVERAGE_GAPS to avoid confusion
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
Mauricio Carneiro
Eric Banks
Ryan Poplin
Joel Thibault
David Roazen
Guillermo del Angel
Khalid Shakir
Roger Zurawicki