ggCaller v1.2.2

Minor updates to v1.2.1:

• Clears DBG and traversed path objects from memory before gene overlap analysis.
• Reduces memory requirements in overlap graph traversal.

Bug fixes:

• Corrects colour update issue when outputting gene sequences.

ggCaller v1.2.0

Major updates to v1.1.1:

• Incorporates Balrog models for scoring of genes. This greater improves gene call specificity.
• Incorporates directed acyclic graphs for calculation of compatible high-scoring ORFs based on overlaps.

Bug fixes:

• Fixes issue where not all viable ORFs returned due to assumption of ORF strandedness being the same as node strandedness. ORF strandedness now calculated using relative node standedness.

ggCaller v1.1.1

Minor fixes to v1.1.0:

• Updates CMakeLists.txt to enable location of pthreads, bifrost, zlib and openMP libraries
• Implements opting-out of FMindex filtering when using a pre-built graph through --not-ref (was opt-in previously through --is-ref)

ggCaller v1.1.0

This is a major update which ports ggCaller functionality into C++ from Python.

New features:

• Build Bifrost graphs directly from sequence data (genomes, reads or both)
• Read and analyse pre-built Bifrost graphs
• Speed improvements, including more efficient graph traversal, use of robin-hood maps and parallelisation
• Changes to fasta output headers for easier parsing
• Enabling specification of stop and start codons in .json format

First release

First release.
Includes Bifrost graph traversal and FMindexing workflows.
Also includes auto-installation via setup.py.