Helper function to remove reads matched to filter librariesSource:
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.
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
listof target query names from
reads_bamthat have also aligned to a filter reference library. Each
listelement should be a vector of read names.
The name of the .bam or .csv.gz file that to which the filtered alignments will be written.
yieldSize, an integer. The number of alignments to be read in from the bam file at once for chunked functions. Default is 100000.
The number of threads to be used in filtering the bam file. Default is 1.
The aligner which was used to create the bam file.
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
Turns off most messages. Default is
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