search_from_fastq_reads {minSNPs}

search_from_fastq_reads

Description

search_from_fastq_reads identify the matches from a list of search strings

Usage

search_from_fastq_reads(
  fastq_file,
  search_tables,
  skip_n_reads = 0,
  progress = TRUE,
  max_n_reads = -1,
  quality_offset = 33,
  output_temp_result = TRUE,
  temp_result_folder = "./temp_results",
  simplify_id = TRUE,
  output_read_length = TRUE,
  bp = MulticoreParam()
)

Arguments

fastq_file

fastq file containing the runs to search from

search_tables

a dataframe with the following columns: - ["id"],"type",["sequence"],"strand","result","extra","match_ref_seq"

skip_n_reads

number of reads to skip, default is 0

progress

whether to show the progress bar

max_n_reads

maximum number of reads to read, default to -1 (all)

quality_offset

the quality offset to use, default to 33

output_temp_result

whether to output the temporary results

temp_result_folder

directory to output the temporary results

simplify_id

simplify and shorten the read id to the first part

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'.