2.9.8

• Update RefMapOpt.sh

  • Fix bug in reporting of mean number of contigs mapped and mean number of discordant mappings.

• Update dDocent

  • Keep version number updated with RefMapOpt script. No changes to actual dDocent code

Full Changelog: v2.9.7...v2.9.8

2.9.7

Small bug fixes:

• Update small bug when only one contig
• Increase memory to default call of PEAR
• Update dup_sample_filter.sh

2.9.4

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.

2.8.13

fixes #71 which resulted in an inefficient scan of the reference genome to determine if created by dDocent.

2.8.12

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 MAXMemory option. The GNU-Parallel implementation 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.

Version 2.7.8

Update remake_reference.sh script and add version to logfiles

Version 2.7.7

Fixes small bug if assembling data with less than 8 processors.

Version 2.7.6

This release is an incremental update that replaces trimmomatic with 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!

Version 2.6.0

dDocent is now OS X compatible if installed using bioconda

Version 2.5.6

This removes a few outdated dependency checks.