search_from_reads

Source: R/search_from_reads.R

search_from_reads identify the matches from a list of search strings

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`.