TagOtherFileByName #
Mark reads based on wether names are present in another file.
[[step]]
action = "TagOtherFileByName"
segment = "read1" # which name are we using
label = "present_in_other"
filename = "names.fastq" # Can read fastq (also compressed), or sam/bam files
false_positive_rate = 0.01 # false positive rate (0..1)
seed = 42 # seed for randomness
ignore_unaligned = false # in case of BAM/SAM, whether to ignore unaligned reads
readname_end_chars = " /" # (optional) chars at which to cut read names before comparing. If not set, no cutting is done.
This step makrs reads by comparing their names against names from another file.
With false_positive_rate > 0, uses a cuckoo filter, otherwise an exact hash set.