## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----CommunityProfiling, eval = TRUE------------------------------------------ library(Rbec) fq <- system.file("extdata", "test_raw_merged_reads.fastq.gz", package="Rbec") ref <- system.file("extdata", "test_ref.fasta", package="Rbec") Rbec(fq, ref, tempdir(), 1, 500, 33) ## ----Contam_detect, eval = TRUE----------------------------------------------- log_path <- list.files(paste(path.package("Rbec"), "extdata/contamination_test", sep="/"), recursive=TRUE, full.names=TRUE) log_file <- tempfile() writeLines(log_path, log_file) Contam_detect(log_file, tempdir())