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CHANGELOG.md

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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