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Filter an alignment (BAM-file).

Source: R/refgenome.R
BascetFilterAlignment.Rd

This is typically used to either remove host DNA, or keep reads mapping to a known reference

Usage

BascetFilterAlignment(
  bascetRoot,
  numLocalThreads = 1,
  inputName,
  outputName,
  keep_mapped = FALSE,
  overwrite = FALSE,
  runner = GetDefaultBascetRunner(),
  bascet_instance = GetDefaultBascetInstance()
)

Arguments

numLocalThreads

Number of threads to use for each runner

outputName

Name of output file (BAM-file)

keep_mapped

Keep the mapped reads (TRUE) or unmapped (FALSE)

Details

If the BAM-file has paired reads then BOTH reads need to be mapped (flag 0x2); otherwise (flag 0x4)