This release of dDocent changes the implementation of mapping interval creation that is used for variant calling and parallelization. dDocent will now require BEDOPS for mapping interval creation, as it provides a significant saving in both memory and processing time. Mapping interval creation is memory intensive and has proven to be choke point in some analyses relative to hardware capabilities. This version should help alleviate a lot of memory issues. Biggest code changes happened with merged pull #74.
Big thanks to @pdimens for implementing and testing these changes.
This version bring minor bug fixes and several improvements:
- Better and more even memory management for genotyping
- Sorted reference sequences
- Bug fix in PE assembly responsible for a small percentage of misassembled loci when F and PE reads overlapped.
- The deprecation of the
GNU-Parallelimplementation does not actually limit memory usage and can cause failed genotyping instances. The better memory management strategy implemented in this update should alleviate major memory issues.
This release is an incremental update that replaces
fastp for quality and adapter trimming.
fastp is faster, does not rely on a java Environment, and can automatically detect adapters without relying on a list (that also must be installed).
Read trimming is now much faster, and the dDocent environment and dependency list is lighter!
This update is largely internal changes to speed up performance and to increase code portability.