From 1cd8d3b2387d3f93fa23f6ab6e3acf9400855785 Mon Sep 17 00:00:00 2001 From: Arjun Biddanda Date: Mon, 25 Oct 2021 10:18:19 -0400 Subject: [PATCH] updated inline doc-string for prepare decoding for defining inline decoding quantiles --- src/__init__.py | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/src/__init__.py b/src/__init__.py index f03065c..906fee4 100644 --- a/src/__init__.py +++ b/src/__init__.py @@ -51,13 +51,17 @@ def prepare_decoding( Calculate decoding quantities. If a csfs_file is specified, the precalculated CSFS will be used. If no csfs_file is specified, CSFS will be calculated. - :param demography: the demographic file or code (e.g. 'CEU') - :param discretization: the discretization file or discretization quantile information - :param frequencies: the frequencies file, or built-in (e.g. 'UKBB') - :param csfs_file: optional file containing precalculated CSFS (default, CSFS will be calculated at runtime) - :param file_root: optional file root containing data from which frequencies may be calculated - :param samples: number of samples (default 300) - :param mutation_rate: the mutation rate (default 1.65e-8) + :param str demography: the demographic file or code (e.g. 'CEU'), + NOTE: Effective population size is specified as haploid. + :param discretization: a discretization file or discretization quantile information, + for example `[[30.0, 10], [100.0, 8], 25]` specifies a discretization with + 10 intervals of size 30 generations, followed by 8 intervals of size 100, + followed by 25 additional quantiles from the coalescent distribution + :param str frequencies: the frequencies file, or built-in (e.g. 'UKBB') + :param str csfs_file: optional file containing precalculated CSFS (default, CSFS will be calculated at runtime) + :param str file_root: optional file root containing data from which frequencies may be calculated + :param int samples: number of haploid samples (default: 300) + :param float mutation_rate: the mutation rate per basepair per generation (default: 1.65e-8) :return: a decoding quantities object """ return prepareDecoding(