Preprocess Dorado inputs for ninetails cDNA analysis

This function prepares inputs for the cDNA pipeline by processing BAM files, Dorado summary files, and extracting both basecalled sequences and poly(A) signals from POD5 files. Unlike the DRS pipeline, this function additionally extracts basecalled sequences from BAM files for read orientation classification.

Usage

preprocess_inputs_cdna(
  bam_file,
  dorado_summary,
  pod5_dir,
  num_cores,
  qc,
  save_dir,
  prefix,
  part_size,
  cli_log
)

Arguments

bam_file

Character string. Path to BAM file containing aligned cDNA reads with basecalled sequences.

dorado_summary

Character or data frame. Path to Dorado summary file or data frame.

pod5_dir

Character. Directory containing pod5 files.

num_cores

Integer. Number of CPU cores to use.

qc

Logical. Whether to perform quality control.

save_dir

Character. Directory where output files will be saved.

prefix

Character. Prefix to add to output file names (optional).

part_size

Integer. Number of reads to process in each chunk.

cli_log

Function for logging messages and progress.

Value

List containing paths to processed files:

summary_files

Paths to split summary files

bam_files

Paths to split BAM files

sequence_files

Paths to extracted sequence files

polya_signal_files

Paths to extracted poly(A) signal files

Examples

if (FALSE) { # \dontrun{
processed_files <- preprocess_inputs_cdna(
  bam_file = "path/to/aligned.bam",
  dorado_summary = "path/to/summary.txt",
  pod5_dir = "path/to/pod5/",
  num_cores = 4,
  qc = TRUE,
  save_dir = "path/to/output/",
  prefix = "experiment1",
  part_size = 40000,
  cli_log = message
)
} # }