search_from_reads: 'search_from_reads'

In ludwigHoon/minSNPs: Resolution-Optimised SNPs Searcher

search_from_reads

Description

search_from_reads identify the matches from a list of search strings

Usage

search_from_reads(
  all_reads,
  search_tables,
  progress = TRUE,
  ID = "S1",
  all_qualities = NULL,
  output_temp_result = TRUE,
  temp_result_folder = "./temp_results",
  output_read_length = TRUE,
  bp = MulticoreParam()
)

Arguments

all_reads	The reads containing the runs to search from
search_tables	a dataframe with the following columns: - ["id"],"type",["sequence"],"strand","result","extra","match_ref_seq"
progress	whether to show the progress bar
ID	the ID to use, default to S1
all_qualities	quality data, default to NULL
output_temp_result	whether to output the temporary results
temp_result_folder	directory to output the temporary results
output_read_length	whether to output the read length, NULL - do not output; csv - output to csv file; data - output to result
bp	BiocParallel backend to use for parallelization

Value

will return a list of dataframe containing: - 'search_id', 'sequence', 'reads', 'raw_match', 'mean_qualities', 'indexes'.

ludwigHoon/minSNPs documentation built on March 25, 2024, 11:54 a.m.