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Version 2.7.5
* BUGFIX: be aware of the primer3 version, and treat the output differently
Version 2.7.4
* BUGFIX: return with an error message when a FASTA header contains a tab
Version 2.7.3
* FEATURE: -b option to use tblastn algorithm instead of megablast (for distant genomes)
* FEATURE: -t options to use more than one blast thread (useful for large genomes)
* FEATURE: -n option to regulate the distance between adjacent contigs
* BUGFIX: a cleaner "--version" output
Version 2.7.2
* BUGFIX: correctly import pre-made blast outputs (-p)
Version 2.7.1
* FEATURE: two new files to detail the position of the unaligned regions (-M)
Version 2.7
* FEATURE: new option to modulate the multiple replicons conflicts (-R)
* FEATURE: new option to obtain also the inner primers (-I)
* BUGFIX: multiple replicons collision bugfixes
* BUGFIX: better BioPython version check
Version 2.6.2
* FEATURE: check the input files format
Version 2.6.1
* BUGFIX: Sanitize Blast inputs when files or sequences names contain non-standard chars
Version 2.6
* FEATURE: PDF maps in each "Map_" folder (BioPython >= 1.59 is needed)
* FEATURE: -B and -L values can be set below the suggested minimum values
* FEATURE: -N option to generate the maps without the 100 Ns between each contig
* BUGFIX: Coverage option (-C) now working as expected
* BUGFIX: One base misplacement of contigs in ACT maps
* BUGFIX: No overlap check when there is only one contig mapped
* DEPRECATION: -I option removed
* OTHER: Some credits to recent contributors
* OTHER: Changelog file added
Version 2.5.0
* FEATURE: PCR primers are computed from the last contig to the first one
* FEATURE: Overlaps between contigs are checked using Blast
* FEATURE: Notifications and better errors handling
* BUGFIX: Unused imports clean-up
* BUGFIX: Code header clean-up
* OTHER: Some credits to recent contributors
Version 2.3.3
* BUGFIX: Older biopython versions support: SeqIO write method may require a list
Version 2.3.2
* BUGFIX: Correct map directory name for the ACT scripts
Version 2.3.1
* BUGFIX: Make Blast suport any kind of sequences IDs
* BUGFIX: Clearer messages on Blast failures
Version 2.3
* FEATURE: Generation of embl files instead of fasta AND tab files (just three files are needed by ACT now)
* FEATURE: An easier way to open the ACT maps is now implemented script are generated in each "Map_" directory the maps can be automatically opened (-l option)
* BUGFIX: Support for Biopython 1.57+
* BUGFIX: EMBL files no more causing crashes of ACT on long contig names
* BUGFIX: PrintStats now gives the correct number of primers
* BUGFIX: Fix two crashes when no contigs are mapped
Version 2.2
* FEATURE: PCRPrimers.tsv is now produced by default (with -P option)
* FEATURE: Mapped and UnMapped txt files now contain the molecules length
* FEATURE: The script can be launched from any location now (abacas will be found)
* BUGFIX: UnMappedContigs.txt now is correctly created
* DEPRECATION: The abacas generated outputs after primer picking are not used anymore
* DEPRECATION: is no longer produced as an output
Version 2.1
* FEATURE: UnMappedContigs.txt file
* FEATURE: file
* FEATURE: More outputs with -M option:
* Four fasta files with aligned/unaligned regions (on contigs and reference)
* PCRPrimers.tsv, containing details about the generated primers
* BUGFIX: Remove those primers generated because of Ns regions INSIDE a contig
* BUGFIX: Fail-safe printing of statistics
* DEPRECATION: Use of legacy-blast now gives a deprecation warning
Version 2.0
* REFACTOR: Contig profiling and mapping use only Blast
* REFACTOR: Abacas and Mummer are used only for primer picking
* REFACTOR: Removed deprecated functions and added new classes
* FEATURE: New "map" file (MappedContigs.txt), containing the contigs mapped to the reference
* BUGFIX: Minimum contig length and minimum big hit length now have a minimum size
Versions 1.x
* 1.0.1 BUGFIX: removing underscores from contig names
* 1.1 FEATURE: added a tblastn from proteins in reference molecules with no homology
* 1.2 BUGFIX: Handling primer3 newer versions // Removed "Linear" option
* 1.3 BUGFIX: Unused splitted contigs correction
* 1.4 FEATURE: added the -A option to automate the primer design parameters input // Various bugfixes
* 1.4.1 BUGFIX: prevention of crashes during PrintStats function
* 1.4.2 FEATURE: added the -G (DEBUG) option // Check for really old BioPython versions
* 1.4.3 FEATURE: add a prefix to the generated directories (-f option)
* 1.4.4 BUGFIX: a little bugfix on prefix option