First Version on Github.
- Added more mitochondrial reference sequences.
- Multiple amino acid references can now be analyses in one run. Input sequences will be assigned to the reference for which it has the highest score. If scores are equal, input sequences will be added to multiple references.
- Now multiple fasta file and multiple fastq will can be specified. They will be merged before being analysed. The old -d and new -q option are now MultiArg options.
- A new opion was added: --temporaryDirectory , --keep-concat-input-file
- refactored the code for future changes.
- Fixed bugs that could result in crashes with segmentation fault. I have so far not found changes in the output, but I cannot exclude this at the moment.
- currently, the changes are only in the new branch https://github.com/cmayer/MitoGeneExtractor/tree/refactor-bugfix-v1.9.6
- Now uses version CSequences3.1.h together with CSequence_Mol3.1.h. Several improvements in these files.
- In the fastq to fasta converter, the program stopped if reads had different lengths. This was due to the fact that we used the add_sequence_to_alignment element function. This was modified and renamed to add_sequence_to_dataset, which does not check the lengths of the sequences. This change was made in CSequences3.1.h.
- Modified the progress and debug output.