New change log (#256)

* Add and update change.log.md to unify change.log and release notes

* Rename changelog file

CHANGELOG.md

@@ -0,0 +1,88 @@
+## Release Notes
+
+### develop
+
+* Lots of new features and bug fixes are added to the develop branch, which is generally stable. Consider trying it out.
+
+#### latest changes in develop
+
+* CHANGE: HTSLIB 1.3.1+ is now required
+* FEATURE: added `dng treecall` v2
+* FEATURE: new k-alleles model for `dng call` that improves mutation calling
+* BUGFIX: memory leak fixed with when using BCFtools parsing functions
+* FEATURE: improved `dng pileup` now supports slurping regions and filter in number of alleles
+* FEATURE: added region specification with BED files when using VCF on `dng call` 
+* FEATURE: added support for AD/TAD format in `dng call` and `dng loglike`
+* FEATURE: updated version of external dependencies
+* FEATURE: improved support for regions in BAM files
+* FEATURE: `dng dnm` can now handle indels 
+* BUGFIX: fixed segfault found in some cases when using `GCC 4.8` 
+* FEATURE: improved compiling on Apple
+* FEATURE: optimized peeler implementation and interface
+
+### 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.
+
+### v0.5
+
+* switched to cmake
+* separate models for X chromosome calling in male offspring, female offspring
+
+### v0.4
+
+* paired sample analysis
+* parental phaser
+
+### v0.3
+
+* INDEL length based mutation prior
+* look at additional trio configs compared to initial version
+
+### v0.2
+
+* incorporated BCF parser
+* denovo INDEL calling

README.md

@@ -342,59 +342,6 @@ dng treecall genotype -t output.best.tree samples.vcf output.gtcall
 dng treecall annotate -t output.best.tree samples.vcf output.gtcall output.best.annotated.tree
 ```
 
-## Release Notes
-
-### develop
-
-* Lots of new features and bug fixes are added to the develop branch, which is generally stable. Consider trying it out.
-
-### 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.
-
 ### dng treecall: Finding Mutations and Trees from Single Cell Sequencing
 
 `dng treecall` is an experimental module to identify mutations and trees from whole-genome sequencing of single cells