We have looked into the memory consumption of some of the processes and optimised them. `vcf2fasta` can run locally for many many VCFs without running out of memory and crashing. `filter_vcf` runtime has also been improved, along with memory utilisation.
- Memory optimisations: 12
- Annotating variants is also optimised to use only the momery required.
- Fixed issue with **N** in the reference where we have to insert it for mpileup to work., 13.
- `samtools sort` is supplied with -m option if there is at least 1G of memory per CPU. When there is enough memory, sort will be done in-memory, instead of temp files.
- `--with-mixtures` option allows to output IUPAC extended alphabet mixture codes, for SNP positions that **FAIL** filters, based on frequency threshold. E.g. if threshold is set to 0.2, and record is A:50,T:50 for _REF_ and _ALT_, then both are used because for each base mixture is 0.5. However, if A:2, T:98, then only T is used because A's ratio is 0.02. Multi ALT bases are also treated in the same fashion.
- Progress for `vcf2fasta` based on guestimate of total number of records
- Bug fixes