ggCaller v1.4.3

Minor update to v1.4.2

• Removes -march=native compiler flag from CMakeLists.txt

ggCaller v1.4.2

Minor updates to v1.4.1:

• Corrects issue with duplicate entries in GFF that prevent running with Panaroo.
• Updates documentation to encourage use of --gene-finding-only mode.

ggCaller v1.4.1

• Implements iterative gene calling, allowing genes to be called in first pass, and new genomes to be called against the original set
• Reimplements gene clustering algorithm to enable iterative clustering, removing multiple passes through clusters with a single greedy pass
• Adds '--gene-finding-only' option to output gff3 files compatible with Panaroo input
• Adds intermediate file writing to reduce memory consumption
• Replace '--data' with '--prev-run' option to allow for iterative updates of gene calls when analysing new genomes
• Updates unitig annotation pipeline to function with new iterative functionality
• Updates documentation with changes to iterative gene calling

ggCaller v1.3.7

Minor updates to v1.3.6:

• Corrects out of range error during contig mapping due to 'empty' contig as in issue #35

ggCaller v1.3.6

Minor updates to v1.3.5:

• Corrects deprecation warning with Biopython v1.80

ggCaller v1.3.5

Minor updates to v1.3.4:

• Corrects issue with generating core genome alignment with pan option
• Converts FM-index to uppercase to avoid indexing issues and GFF generation
• Adds docker build continuous integration
• Corrects installation check issue with latest version of HMMER 3.4
• Adds manual download and specification of ggCallerdb (BALROG and annotation databases)

ggCaller v1.3.4

Minor updates to v1.3.3:

• Corrects issue with over-clustering during mistranslation correction.
• Sets default annotation to "fast"

ggCaller v1.3.3

Minor updates to v1.3.2:

• Fixes issue with linking of torch library.

ggCaller v1.3.2

Minor updates to v1.3.1:

• Addresses bug where core genome alignment fails if one sequence has no core genes.
• Changes naming of alignment files from gene name to centroid name for ease of parsing.

ggCaller v1.3.1

Minor updates to v1.3.0:

• Adds start-site kmer-ization to improve sensitivity of matches across colours.
• Adds start-site score tolerance to check shorter ORFs with certain probability or greater of being real (based on stop-codon coverage).
• Bug fixes.