Bug fixes
- We now recommend setting RevertSam's
VALIDATION_STRINGENCY
to LENIENT or SILENT if SAM records do not validate and the reversion will obviate the failures (#858). - Fingerprinting tools introduced a bug where if platform unit (PU) was undefined, the tool would error. Now the tools allow for an empty PU attribute (#885).
- DownsampleSam's
METRICS_FILE
argument is now optional instead of required (#884).
For developers
- Instead of using idiosyncratic ordering, IlluminaDataProviderFactory's
availableTiles
now sorts CBCL tiles for predictable handling, e.g. when parallelizing processes (#878).