Extract Barcodes from BAM File — barbac

This function extracts barcode sequences from a BAM file based on the specified reference name and position range, and saves the result as a clean CSV file.

Usage

barbac_xtr(
  bam_file,
  ref_name = "Reference_barcodes",
  start_pos = 54,
  end_pos = 78,
  output_file = NULL,
  min_count = 1,
  verbose = TRUE
)

Arguments

bam_file: Character string. Path to the BAM file from which to extract barcodes.
ref_name: Character string. Name of the reference to be used. Default is "Reference_barcodes".
start_pos: Numeric. Start position of the barcode in the reference. Default is 54.
end_pos: Numeric. End position of the barcode in the reference. Default is 78.
output_file: Character string or NULL. Path for output CSV. If NULL, creates filename based on input BAM file. Default is NULL.
min_count: Numeric. Minimum count threshold to include a barcode. Default is 1.
verbose: Logical. Print progress messages. Default is TRUE.

Value

A character string with the path to the generated CSV file.

Details

This function:

Reads aligned sequences from a BAM file at specified genomic coordinates
Extracts barcode sequences from the specified region
Counts occurrence of each unique barcode
Filters by minimum count threshold
Saves results to CSV with columns: barcode, counts, barcode_length

Examples

if (FALSE) { # \dontrun{
# Extract barcodes from default region
barbac_xtr("sample1_sorted.bam")

# Extract from custom region
barbac_xtr(
  bam_file = "sample1_sorted.bam",
  ref_name = "chr1",
  start_pos = 100,
  end_pos = 125
)

# Specify output file and filter low counts
barbac_xtr(
  bam_file = "sample1_sorted.bam",
  output_file = "sample1_filtered_barcodes.csv",
  min_count = 5
)
} # }