Releases: bioinform/varsim
Releases · bioinform/varsim
VarSim 0.6.2
- Added option
-outdir
to vcf2diploid tool to specify output directory. - Added an experimental script
generate_small_test_ref.py
for simulating specific regions of the genome. The script will generate a restricted reference FASTA and truth/sampling VCFs based on the input regions in BED format. - Fixed a bug which would cause empty alleles to be output in some cases.
VarSim 0.6.1
- Fix incorrect liftover of intervals
- Add preliminary support of supplementary alignments in BAM validation
- Remove reference as a required argument
VarSim 0.6
- Added support for arbitrary read names from read simulators. The true alignments can be encoded in a separate file which is essentially a dictionary mapping from read names to true locations.
- samcompare tool now outputs BAMs to save space.
- Code refactoring and cleanup.
VarSim 0.5.3
- Added specificity computation.
- Fixed bug in
varsim_somatic.py
when calling randvcf2vcf tool. - Added
--somatic_vcfs
option tovarsim_somatic.py
. This option is used to provide hard-coded somatic variants to be used in building the ground truth. - Fix logging for
varsim_somatic.py
to avoid mixing logs whenvarsim.py
is invoked fromvarsim_somatic.py
. - The generated truth VCF has a more complete header now and is sorted.
VarSim 0.5.2
- Fixed duplicate read name bug
- [Unsupported] Add constraints to variantcompare
VarSim 0.5.1
- Fix bug(s) in IntervalTree
- More filtering options for results
- [Unsupported] Simple pacbio support
VarSim 0.5.0
- Support all chromosomes
- Improved BED file filtering
- Add SV counts to log file
- Reformatting
- Change command line arguments a bit
- Fix bug in alignment plots
VarSim 0.4.1
- Fix some interval tree bugs, all squished now I hope
- Option to enable comparing genotypes
- Option for multiple samples
VarSim 0.4
- New Interval tree implementation
- Use HTSJDK
- Various bug fixes
VarSim 0.3.4
fixed some internal code about JSON escaping