ntLink v1.3.10

• Release v1.3.10
• Bugfix for overlap detection
  • Fixing an edge case - was possible for the trim coordinates to be invalid (5' trim coordinate to be greater than 3' coordinate), leading to unexpected coordinates in the AGP file
  • Now, if this case is detected, omit sequence and revert to a gap instead
• Make installation paths to the ntLink scripts more flexible
  • If the scripts are found in the same directory as the ntLink Makefile, then use this path. Otherwise, revert to the previous behaviour and look for the files in directories relative to the Makefile
• Documentation updates

ntLink v1.3.9

• Release v1.3.9
• Fix gap-filling code to use multiple long reads files, if provided (#84)
  • Gap-filling code was expecting a single input reads file, but supplying multiple input long read files is a valid input for ntLink
  • Added a test which uses gap-filling and multiple input long read files
• documentation updates

ntLink v1.3.8

• Release v1.3.8
• Bugfix for dev option in ntLink_rounds without gap-filling

ntLink v1.3.7

• Release v1.3.7
• Adds parameter soft_mask. Set soft_mask=True when running ntLink with gap_fill target to use lowercase characters for filled gaps

ntLink v1.3.6

• Release v1.3.6
• Add option to output read to contig mappings in PAF format
  • Invoked by specifying paf=True to ntLink command
• Add error handling to ntLink pairing stage - will clean-up files if there is an error encountered
• Documentation updates
• Bugfixes

ntLink v1.3.5

• Release v1.3.5
• Refactor code in overlap and gap-filling stages to reduce the peak memory usage
• Add option to retain intermediate files when running ntLink rounds (dev=True)
• Add option to run ntLink mappings with increased sensitivity (sensitive=True)
  • It is recommended to keep the default sensitive=False when running ntLink in scaffolding mode, and use sensitive=True when running ntLink mapping for other applications (ex. GoldRush-Edit)
• Bugfixes, code style fixes

ntLink v1.3.4

• Release v1.3.4
• Bugfixes to ntLink_rounds
• Add to CI

ntLink v1.3.3

• Release v1.3.3
• Add additional final soft-links to make final file name consistent when different options specified
• Add extra clean rules for cleaning up intermediate files of ntLink runs
  • More information can be found in the wiki

ntLink v1.3.2

• Release v1.3.2
• Remove packaged btllib, and made it a dependency instead
• Add checks in ntLink for btllib installation

ntLink v1.3.1

• Release v1.3.1
• Fixed bug that could lead to a file name collision at the gap-filling stage when running parameter sweeps in the same directory
• Changed PYTHONPATH assignment in ntLink makefile to append to existing PYTHONPATH environment variable, not overwrite it
• Documentation updates