## ----echo=FALSE, results="hide"----------------------------------------------- options("knitr.graphics.auto_pdf"=TRUE, eval=TRUE) ## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("Rbwa") ## ----loading, eval=TRUE------------------------------------------------------- library(Rbwa) ## ----build_index, eval=TRUE--------------------------------------------------- dir <- tempdir() fasta <- system.file(package="Rbwa", "fasta/chr12.fa") index_prefix <- file.path(dir, "chr12") bwa_build_index(fasta, index_prefix=index_prefix) list.files(dir) ## ----bwa_aln, eval=TRUE------------------------------------------------------- fastq <- system.file(package="Rbwa", "fastq/sequences.fastq") bwa_aln(index_prefix=index_prefix, fastq_files=fastq, sai_files=file.path(dir, "output.sai")) ## ----bwa_aln2, eval=TRUE------------------------------------------------------ bwa_aln(index_prefix=index_prefix, fastq_files=fastq, sai_files=file.path(dir, "output.sai"), n=3, k=3, l=13) ## ----bwa_sam, eval=TRUE------------------------------------------------------- bwa_sam(index_prefix=index_prefix, fastq_files=fastq, sai_files=file.path(dir, "output.sai"), sam_file=file.path(dir, "output.sam")) ## ----reading1, eval=TRUE------------------------------------------------------ strtrim(readLines(file.path(dir, "output.sam")), 65) ## ----bwa_sam_multi, eval=TRUE------------------------------------------------- xa2multi(file.path(dir, "output.sam"), file.path(dir, "output.multi.sam")) strtrim(readLines(file.path(dir, "output.multi.sam")), 65) ## ----bwa_mem, eval=TRUE------------------------------------------------------- fastq <- system.file(package="Rbwa", "fastq/sequences.fastq") bwa_mem(index_prefix=index_prefix, fastq_files=fastq, sam_file=file.path(dir, "output.sam")) ## ----reading2, eval=TRUE------------------------------------------------------ strtrim(readLines(file.path(dir, "output.sam")), 65) ## ----------------------------------------------------------------------------- sessionInfo()