- Version 1.1.1
- remove pysam as requirement
- Version 1.1.0
- Made compatible with both python 2 and 3
- Added Conda installation with all dependecies
- Command changed from
python ./src/isafe.py [Options]toisafe [Options]
- Version 1.0.7
- Fix bug for reading indexed BCF files
- Raise error in create_rolling_indices() in isafeclass.py when total number of variants is smaller than --window
- Raise error when --window is smaller than --MinRegionSize-ps
- Raise error when --window is smaller than --step
- Print version (-v, --version)
- Version 1.0.6
- Fixed bug with numerical sample names.
- Version 1.0.5
- If the ancestral allele file (--AA) is not available the program raises a warning and assumes reference allele (REF) is ancestral allele.
- Version 1.0.4
- Raise error for inconsistent ploidy, non-biallelic, and empty region.
- Version 1.0.3
- Handling male (haploid) samples for chromosome X.
- Version 1.0.2
- Track execution progress and fixing minor bugs.
- Version 1.0.1
- Keeps not SNPs (indels, MNPs, and etc) as long as they have only one ALT (binary alleles).