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 to varsim_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 when varsim.py is invoked from varsim_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