Code

amrfinder correct for read counts#188

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andrewdavidsmith merged 8 commits intomastersmithlabcode/dnmtools:masterfrom amrfinder-correct-for-read-countssmithlabcode/dnmtools:amrfinder-correct-for-read-countsCopy head branch name to clipboardNov 28, 2023

+123-142

Commits

Commits on Nov 27, 2023

• smithlab_cpp: updating submodule

  andrewdavidsmith

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• amrfinder: added an option to turn off the correction to likelihood for the number of reads which is applied to the likelihood for the two alleles model

  andrewdavidsmith

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• EpireadStats.hpp: changing the EpireadStats class to struct and allowing default values for default constructor. Also adding an instance variable to indicate whether log likelihood for allel pair m…

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  andrewdavidsmith

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• EpireadStats.cpp: adding a variable to control the use of correction to the allele pair model log likelihood based on number of reads

  andrewdavidsmith

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• amrfinder.cpp: Using the default constructor for EpireadStats

  andrewdavidsmith

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• amrtester: using an approach more similar to amrfinder which uses the EpireadStats class instance and allows a correction for read count for the allel pair model log likelihood

  andrewdavidsmith

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Commits on Nov 28, 2023

• amrtester: more changes

  andrewdavidsmith

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• md5sum: update for the empty amr file output by amrfinder currently

  andrewdavidsmith

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