VarSim 0.7.7

• minor bug fix for quickstart.sh

VarSim 0.7.6

• added distance-based metrics for VCF comparison in logging
• minor fix for example

VarSim 0.7.5

fixed bugs related to the following issues

• varsim.py child process control
• missing GT
• MNP cannonicalization
• multiple variants at the same loci
• interval tree building with duplicate intervals (esp 1-bp interval)

VarSim 0.7.4

Bug fix for fastq liftover.

VarSim 0.7.3

• bug fix for VCFCompare and RandVCFGenerator

VarSim 0.7.2

• Fixed some bugs in VCF parsing and alignment validation
• Refactoring for SAMCompare class
• Tests for SAMCompare

VarSim 0.7.1

• Fixes the build release script to also include liftover_restricted_vcf_map.py
• Updates VarSim version in quickstart.sh
• Fix for empty REF being generated in some cases
• Uses java -jar VarSim.jar -version to extract version in the Python scripts

VarSim 0.7.0

This is an experimental release!

Multiple enhancements and bugfixes including:

• Support for simulating and validating translocations.
• Several test cases have been added to the Java code.
• BED-based FASTA and VCF restriction script generate_small_ref.py now has a flag to generate sequential contig names instead of <chr>_<start>_<end> naming.
• Refactoring and clean up of the code.

VarSim 0.6.3

Bugfixes

• Fixed NullPointerException due to missing some categories of variants.

VarSim 0.5.4

Bugfixes for version 0.5.3

• Made reference an optional parameter
• Fixed NullPointerException due to missing truth for certain categories of variants.