SmooshAndAdd shouldn't be a method #7
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Closed by 98583d6 |
dunleavy005
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Jun 22, 2018
* some Simple/Phylo interface merging * cleaned up GermlineGene class * more class changes * EmissionData class changes * slight Germline name changes * TONS of interface changes * Minor changes in docs and comments. * slight changes reflecting Erick's comments * more small changes * Germline changes * small Chain changes * fixing name in Germline * made non-emission and emission match matrices * test commit to check build failure * Updating eigen submodule. * removing unnecessary code + improving readability * clearer match_indices_ indexing * adding pre_marginal_ to Smooshable + small changes * adding Germline pointer to Smooshable + typedef'ing Germline pointers * added function to make pile dirty * added function that finds dirty smooshables * added left_flexbounds_name to Germline-encoded Smooshables * Pile updater complete! * comments for PhyloData Pile Updater * changes to Pile Updater comments * moving Simple/PhyloData initialization commonalities into Data constructor * a emplace/push_back change for readability * separating match_indices/pile initialization in Data * slight documentation change * germline xMSA indexing * added GermlineType enum * fixing build error from previous commit * NTI xMSA indexing * xMSA/xMSA rate vector construction * added PhyloData accessors * added PhyloData EmissionVector function * changed EmissionVector to GermlineEmissionVector * fixed NTIProbMatrix * minor changes * letting V/JSmooshables have row/column marginal matrices * fixed the Smooshable updater to account for NTI Smooshables * reinstated Germline tests * reinstated NTInsertion tests * reinstated Smooshable/Chain tests * reinstated Pile tests * made the basic SimpleData tests * made the SimpleData Pile tests * reinstated BCRHam tests * removed obsolete tests * some PhyloData tests * submodules update * pt finally is hooked up with linearham! * bunnyhutch account pushes? * changed alphabet structure + various small changes * IGNORE ME! * Tree initialization stuff (no tests) * small Smooshable chage * adding partition object to PhyloData + some basic tests * added PhyloData Pile tests * adding brent library * added brent optimization functor template * PhyloData now holds unique_ptr<Partition> + branch_optim_func changes * small changes * marginal likelihood calculator * switched submodules (pt -> libptpll) * fixing wercker.yml file * another wercker fix * dont give up! * added cleaning check to Data::MarginalLogLikelihood * libptpll tip changes * attempt at wercker fix * another wercker attempt * added single branch optimization functions * one-pass branch length optimization function * wercker fix attempt * wercker fix attempt again * wercker fix attempt againagain * wercker fix attempt againagainagain * wercker fix attempt try * libptpll/wercker.yml changes * full branch length optim. function * added brent upper bound calculations * added libptpll changes * modified brent left bound + made branch optimization public * small changes * re-shuffled data folders + added branch length optimization test * forgot to commit new data files * added function for finding SPR regraft branches * fixed SPR regraft function * wercker bot fix * wercker bot fix #2 * wercker bot fix #3 * wercker bot fix #4 * wercker bot fix #5 * wercker bot fix #6 * wercker bot fix #7 * wercker bot fix #8 * oh my god, is the wercker bot werckinggit diff * Ok now wercker bot shall werck werck werck * added raxml-ng submodule * initial raxml-ng commit * deleted raxml-ng submodule * Revert to wercker commit * adding libpll dependency * deleting unnecessary libraries/code * Germline, linalg, utils edits * slight change * cleaned up NTInsertion * small fix * cleaning NPadding code * reinstating VDJGermline * re-instated smooshable/pile tests * reinstated SimpleData tests * deleting SPR functions * Removed unstable submodule Eigen * added stable Eigen submodule * updated submodules * Removed submodule libpll * re-instated PhyloData tests * tests new-lining * re-organized PhyloData data files * added Amrit correction + new phylo likelihood test * deleted comment
dunleavy005
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Nov 21, 2018
* forward algorithm only should run once * removed 'init_scaler_count' variables * changing fn name * change from 'resize' to 'assign' * added naive sequence sampling! * re-ordering 'naive' to be 1st taxa * changed partis cached data variable * unified MSA for [Simple|Phylo]HMM + SimpleHMM now does star-tree likelihood * added naive seq sampling tests * RevBayes tree reader * linearham tree writer * unnecessary getter fn * fixed handling of RevBayes trees * removed 'Posterior' column from revbayes example TSV * switching header order * forward probs re-compute with new tree * 'const'ing some member fns * refactored the tree writing code * added 'caache_forward' to tests * added 'cache_forward' and RB tree stuff to tests * EPS modification * updated submodules * handling missing branch lengths * wercker fix #1 * wercker fix #2 * wercker fix #3 * wercker fix #4 * wercker fix #5 * wercker fix #6 * wercker fix #7 * adding header to utils.cpp * wercker fix #8 * wercker fix #9 * wercker fix #10 * wercker bot wercksgit add wercker.yml ! * fixed burnin mechanism * now a one-pass procedure * updated phylolikelihood in R * moved utility functions to utils.*pp * add TCLAP submodule * removed burnin handling * added functionality for cmd-line sampler + revbayes batch inference * fixed comments * variable name change * fixed tree destructor in PhyloHMM * added linearham executable * comment fix * updated submodules * cleaning up root dir * added doxygen comments for VDJGermline and utils * adding assert header * added HMM doxygen comments * moved linalg.*pp to utils.*pp * small comment changes * added SimpleHMM doxygen comments * fixed some doxygen comments * comment change * removed word 'range' from comment * added PhyloHMM doxygen comments * updated Doxyfile * unnecessary README * gh-pages deploy * added weighted bootstrap w/ ASR script * wercker fix #1 * wercker fix #2 * wercker fix #3 * wercker fix #4 * wercker fix #5 * wercker fix #6 * wercker fix #7 * wercker fix #8 * wercker fix #9 * wercker fix #10 * wercker fix #11 * wercker fix #12 * added graphviz to wercker * try fix * break on purpose * unbreak wercker * modified SConstruct comments * added RevBayes template * README updates. * added RevBayes templater script * added partis submodule * partial scons-nestly pipeline * fixed wercker.yml * now fixed wercker.yml * now fixed wercker.yml again * now fixed wercker.yml again again * THIS BETTER WORK * THIS BETTER WORK UGHH * PRAY TO GOD * try wercker again * fix wercker build FOR REALZZZZ * minor tweaks * small tweak * added RevBayes submodule * added RevBaves inference step * wercker webhook check * wercker webhook check #2 * wercker check * wercker update too slow - stop for now * added 'num_rates' to revbayes step * let RevBayes exit if reading data fails * spelling change * added intermediate linearham scons target * added final linearham scons target * wercker fix start * adding libz-dev * adding libncurses-dev * adding libyaml-cpp-dev * adding numpy * adding colored-traceback * adding psutil * adding scipy * adding dendropy * adding dendropy again * adding pysam * checking HOME * worth a try * whoops * whooops * now try * now tryy * now tryyy * check the wercker env * manually export HOME * partis fixed so HOME isnt required * add matplotlib * try building linearham without yaml-cpp * fixed NPadding transition checking * removed submodule yaml-cpp * no more yaml-cpp source build * added liao (2013) example dataset * adding Dockerfile template * only build revbayes * only build partis * Docker can run 'scons --build-deps' * updating submodules * whoops! ASR script did not account for N naive bases * added option to treat FASTA as full CF * updated Dockerfile * install R packages in Dockerfile * removed submodule phylomd * whoops re-added phylomd * removing revbayes build from SConstruct * fully complete Dockerfile! * updated wercker script * fix wercker yaml * i dont always get things wrong, but when i do, its bc of YAML * now? * better! * added germline gene class concepts * added S-W information concepts * added hidden state space concepts * whoops forgot to clang-format ^ * added line to state space section * added hidden state trans prob matrix concepts * added germline padding and emission probability matrix concepts * added scaling concepts * added xmsa concepts * whoops * updated README * Some doxyedits. * updated linearham docs per Erick's comments * more docs update * formula fix * Erick fixes * Final edits on my end. * One more note about the figure. * more edits re: Erick comments * updated submodules * updated partis * updated partis * add a few comments on docs * updated submodules * updated linearham docs
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https://github.com/matsengrp/linearham/blob/master/src/smooshable_chain.cpp#L29
It modifies member data, which is exactly what methods do. Thus it should be a (private) method.
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