change.log

v1.1.1
- FEATURE: When building with cmake, users have the option to download and install dependencies.
Just run `cmake -DBUILD_EXTERNAL_PROJECTS=1 ..`
- FEATURE: `dng help` now fully implemented
- FEATURE: more information added to `dng call` output
- BUGFIX: When running `dng call` with HTSLIB 1.2.1, the following error message was being
emitted: "FIXME: dirty header not synced".  This has been fixed.
- BUGFIX: `dng call` now outputs correct 1-based site locations.
- BUGFIX: a segfault was fixed in `dng dnm` and `dng phaser` caused by invalid commandline arguments
- CHANGE: HTSLIB 1.2+ is now required.
- Miscellaneous improvements to the build system

v1.1
- Main program now called 'dng'
- Added experimental 'dng call' module.
- DeNovoGear now requires HTSLIB 1+, CMake 3.1+, Boost 1.47+, and Eigen 3+.

v1.0
- made changes to indel_mrate parameter
- better indenting
- mu_scale scales indel mutation rate linearly

v0.5.4
- added GPL v3
- updated output fields for indels, snps to be the same 

v0.5.3
- removed 'X' allele in VCF op. VCF can be indexed by Tabix, IGVTools and used in Annovar.	
- added region based denovo calling on BCF files, invoked with	--region flag
- added vcf parser for denovo calling, invoked with --vcf flag


v0.5.2
- Added read-depth, posterior-probability filters.
- Output number of sites in the BCF and number of sites passing filters.
- Modified paired caller output.

v0.5.1
- Fixed bug in triallelic configuration. Some trialleic denovo configurations were being called incorrectly.

ver 0.5.1
- fixed bug in triallelic denovo configurations.

ver0.5
- switched to cmake
- separate models for X chromosome calling in male offspring, female offspring

ver0.4
- paired sample analysis
- parental phaser

ver0.3
- INDEL length based mutation prior
- look at additional trio configs compared to initial version

ver0.2
- incorporated BCF parser
- denovo INDEL calling