Commit 430dddfe authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 3.1.0+dfsg

parent a9e5d64a

.gitignore

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/_deps

/_rev_deps

/unyve



# Meson WrapDB stuff

subprojects/packagecache/

subprojects/googletest*

subprojects/pbbam*

subprojects/pbcopper*

.gitmodules

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[submodule "third-party/pbbam"]

    path = third-party/pbbam

    url = ../pbbam.git

    branch = master

    branch = develop

[submodule "third-party/seqan"]

    path = third-party/seqan

    url = ../seqan.git

    branch = master

    branch = develop

[submodule "third-party/pbcopper"]

    path = third-party/pbcopper

    url = ../pbcopper.git

    branch = master
 
 No newline at end of file
 
    branch = develop

CHANGELOG.md

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# UNANIMITY - CHANGELOG



## [3.1.0]



### Changed

 - Per ZMW timings are default on in DIAGNOSTICS mode or available via hidden

   option --zmwTimings. Output is BAM tag ms



## [3.0.0]



### Refactored

 - MultiMolecularIntegrator renamed to just Integrator

 - MonoMolecularIntegrator removed, all integrators now accept multiple molecules

 - VirtualTemplate removed, as without MonoMolecular it is no longer needed

 - MutatedTemplate added as a View object over some const template

 - Template::Mutate() now returns a MutatedTemplate instead of modifying the Template

 - Template was promoted from a member of Recursor to a member of EvaluatorImpl

 - Recursor refactored to take a template as an argument in most functions

 - Existing model files updated to match the new parent Recursor class

 - s/PB_CHEMISTRY_BUNDLE_DIR/SMRT_CHEMISTRY_BUNDLE_DIR/g



## [2.1.0]



### Added

 - Add Cleric, an alignment reference sequence replacer

 - Add fuse, an alignment consensus caller

 - Add juliet, a minimal minor variant caller

 - Add Fisher's exact test

 - Juliet JSON and HTMl output for HIV-1 pol region

 - Call codon-wise

 - Use pbcopper's q-gram index for sparse alignment

 - Replaced seqan MSA in ChimeraLabeler

 - support loading bundle models from PB_CHEMISTRY_BUNDLE_DIR

   environment variable



## [2.0.4]

CMakeLists.txt

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# CMake build script for the UNANIMITY library

##############################################



cmake_policy(SET CMP0048 NEW)

project(UNANIMITY VERSION 2.1.0 LANGUAGES CXX C)

cmake_minimum_required(VERSION 3.2)

cmake_policy(SET CMP0048 NEW)

project(UNANIMITY VERSION 3.0.0 LANGUAGES CXX C)



set(ROOT_PROJECT_NAME ${PROJECT_NAME} CACHE STRING "root project name")
@@ -16,6 +16,8 @@ ENDIF(NOT CMAKE_BUILD_TYPE) 
# Build-time options

option(UNY_build_bin     "Build binaries." ON)

option(UNY_build_tests   "Build UNANIMITY's unit tests." ON)

option(UNY_build_chimera "Build UNANMITIY's stand-alone chimera labeler." OFF)

option(UNY_build_sim     "Build UNANMITIY's (sub)read simulator." OFF)

option(UNY_inc_coverage  "Include UNANIMITY's coverage script." OFF)

option(UNY_use_ccache    "Build UNANIMITY using ccache, if available." ON)

LICENSE

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Copyright (c) 2016, Pacific Biosciences of California, Inc.

Copyright (c) 2011-2018, Pacific Biosciences of California, Inc.



All rights reserved.