Helper function to remove reads matched to filter libraries

Using the filter_host() function, we align our sequencing sample to all filter libraries of interest. The remove_matches() function allows for removal of any target reads that are also aligned to filter libraries.

Usage

remove_matches(
  reads_bam,
  read_names,
  output,
  YS,
  threads,
  aligner,
  make_bam,
  quiet
)

Arguments

reads_bam

The name of a merged, sorted .bam file that has previously been aligned to a reference library. Likely, the output from running an instance of align_target().

read_names

A list of target query names from reads_bam that have also aligned to a filter reference library. Each list element should be a vector of read names.

output

The name of the .bam or .csv.gz file that to which the filtered alignments will be written.

YS

yieldSize, an integer. The number of alignments to be read in from the bam file at once for chunked functions. Default is 100000.

threads

The number of threads to be used in filtering the bam file. Default is 1.

aligner

The aligner which was used to create the bam file.

make_bam

Logical, whether to also output a bam file with host reads filtered out. A .csv.gz file will be created instead if FALSE. Creating a bam file is costly on resources over creating a compressed csv file with only relevant information, so default is FALSE.

quiet

Turns off most messages. Default is TRUE.

Value

Depending on input make_bam, either the name of a filtered, sorted .bam file written to the user's current working directory, or an RDS file containing a data frame of only requisite information to run

metascope_id().

Details

This function is not intended for direct use.