Package: asmc-asmc
ASMC and FastSMCThis repository contains ASMC and an extension, FastSMC, together with python bindings for both.QuickstartInstall the Python module from PyPIMost functionality is available through a Python module which can be installed with:pipinstallasmc-asmcDocumentationThe following pages of documentation contains specific information:Quickstart guide for usersASMC python docsFastSMC python docsThis Python module is currently available on Linux and macOS.Example Jupyter notebooks showcasing basic functionality can be found here:Example notebooksLicenseASMC and FastSMC are distributed under the GNU General Public License v3.0 (GPLv3). For any questions or comments on ASMC, please contact Pier Palamara using<lastname>@stats.ox.ac.uk.ReferenceIf you use this software, please cite the appropriate reference(s) below.The ASMC algorithm and software were developed inP. Palamara, J. Terhorst, Y. Song, A. Price. High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability.Nature Genetics, 2018.The FastSMC algorithm and software were developed inJ. Nait Saada, G. Kalantzis, D. Shyr, F. Cooper, M. Robinson, A. Gusev, P. F. Palamara. Identity-by-descent detection across 487,409 British samples reveals fine-scale evolutionary history and trait associations.Nature Communications, 2020.ASMC Release Notesv1.3.1 (2023-06-30)Breaking changesNoneOther changesThe location of a.mapor.map.gzfile can now be optionally specified explicitly: previously it was assumed to be at theinFileRoot.v1.3 (2023-03-03)Breaking changesNoneOther changesDecoding a batch can now be done in a selected subregion with from / to indices.
Acm_burn_inparameter takes into account additional variants on either side of the subregion for HMM burn-in.Allow the user to access selected attributes of the DecodingParams and Data from the ASMC object.Python continuous integration now uses Python 3.8 and 3.11 (previously 3.6 and 3.9)Update Catch to v2.13.v1.2 (2021-09-28)All functionality for ASMC and FastSMC is now in this repository (link).Breaking changesFixed an issue with demographic models.
TheCEU.demodemographic model and the decoding quantities for CEU+UKBB previously provided in the repository were mistakenly encoded as diploid rather than haploid.
CEU.demo and CEU+UKBB decoding quantities have now been updated and can be found inthis repository.
Also see the manual for a note on how this affects analyses.Other changesNew API for decoding pairs with ASMC.
In addition to running full analyses as described in the ASMC paper, users can now decode specific pairs and get back a variety of summary statistics.
See theASMC python documentationfor details.New, more extensive,documentationis available.v1.1 (2021-01-20)Legacy repositoryImprovements to documentation and default use.
No changes to any core functionality.Breaking changesThe hashing functionality, previously namedGERMLINE, has been renamed tohashing.
This includes the command line flag for turning this behaviour on/off, which is now--hashing.Other changes--hashingis now ON by default when running the FastSMC executable: previously,--GERMLINEwas OFF by default.Extra output, including the IBD segment length, posterior mean, and MAP, are now on by default.
This behaviour can be toggled with the flags--segmentLength,--perPairPosteriorMeans,--perPairMAP.An example script has been added tocpp_example/FastSMC_example_multiple_jobs.shthat demonstrates how to run FastSMC with multiple jobs simultaneously.The README has been updated to focus on FastSMC functionality.More robust checking is now used to verify the decoding quantities file is correct before reading it.CMake will now, by default, build in Release mode (giving 03 optimisation on Linux).
Previously, Debug was used by default.v1.0 (2020-09-18)Legacy repositoryFirst public release of FastSMC, with functionality as described and used inthis paper.