1.2.2

• Properly calculate Phred averages by first converting the score to a probability before taking the average
• Resolve GoldRush-Path bug where silver and golden paths are not deterministic
• Various QoL changes

1.2.1

• Fixes to make GoldRush compatible with the latest ntLink version (v1.3.11)
• Resolve parameter collisions in goldrush and ntLink makefiles

1.2.0

• GoldPolish-Target now runs as the last step in the default pipeline to polish the soft-masked bases left by ntLink

1.1.2

• Checks reads for invalid bases (non-atcgATCG) and discards them when generating silver paths

1.1.1

• GoldRush now runs in a subdirectory to avoid file clutter and output of each major step are softlinked to top directory

• Output additional information when verbose is turned on

• Simplify spaced seed design specification interaction in goldpath

1.1.0

• Utilize the deterministic version of GoldPolish to generate polished goldtigs
• Require v1.6.2 of btllib

1.0.3

• Packaged btllib removed from the goldrush-path stage
  • This stage now uses btllib as a dependency
• Add ulimit -u to the goldrush-edit stage
  • Increases the maximum number of process to the maximum allowable
  • Addresses a related error that users were reporting
• Update goldrush-edit submodule
  • Added make command to allow for make installation in location other than /usr/bin - this issue was seen when running the docker container on singularity
• Add option to specify shared memory location for goldrush-edit
• Documentation updates

1.0.2

• Detect if no reads pass the Phred and minimum size thresholds for GoldRush-Path and print more informative error message
• Improve error handling for reads parameter in goldrush makefile
  • Detect any error with reads parameter specified and print more informative error message for users
• Update GoldRush-Edit submodule
  • Use new sensitive mapping mode when using ntLink for mappings
• Update test demo
• Documentation updates

1.0.1

• Update goldrush-edit submodule
  • Fixes bug where goldrush-edit would non-deterministically fail
• Add demo for checking GoldRush installation
• Add dev option (development mode) to retain additional intermediate files
• Documentation updates

1.0.0

Results reported in manuscript will use this version