From bf42ac815c03a25bf7987a36a9c59a7846b5e4b6 Mon Sep 17 00:00:00 2001 From: "Juan J. Garcia Mesa" Date: Wed, 11 Apr 2018 00:36:48 +0000 Subject: [PATCH] New change log (#256) * Add and update change.log.md to unify change.log and release notes * Rename changelog file --- CHANGELOG.md | 88 ++++++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 53 ------------------------------- change.log | 58 ---------------------------------- 3 files changed, 88 insertions(+), 111 deletions(-) create mode 100644 CHANGELOG.md delete mode 100644 change.log diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 00000000..45e40d24 --- /dev/null +++ b/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 diff --git a/README.md b/README.md index 18ad8db7..4ba46ec3 100644 --- a/README.md +++ b/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 diff --git a/change.log b/change.log deleted file mode 100644 index b6bed0a9..00000000 --- a/change.log +++ /dev/null @@ -1,58 +0,0 @@ -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