Bug fixes
- The documentation for ScatterIntervalsByNs did not mention that its
REFERENCE
argument must have both an index and a dictionary, and the tool would raise aNullPointerException
if either of these requirements were missing. Now the documentation lists the requirement, and the tool raises more informative errors when either index or dictionary are not present (#881). - The Intel Deflater and Inflater would fail to load, and sometimes cause Picard to hang, on CentOS. Now the Intel tools work on CentOS (#888).
- Upon initialization, the Intel Deflater and Inflater would log an
ERROR
message about missing configuration. Now the log is not produced (#891).
For developers
- New test CommandLineProgramStartupErrorLogTest ensures that default startup logic common to all Picard CLPs does not produce an
ERROR
log (#894).