Function seq_geom_xform::xform_read_pairs_to_fifo
source · pub fn xform_read_pairs_to_fifo(
geo_re: FragmentRegexDesc,
r1: Vec<PathBuf>,
r2: Vec<PathBuf>
) -> Result<FifoXFormData>
Expand description
Given input file paths (possibly multiple sets of files) in r1
and r2
,
and FragmentRegexDesc
geo_re
, this function returns a Result<FifoXFormData>
.
If succesful the Ok(FifoXFormData)
will contain the paths to 2 fifos (1 for each
list of input read files) as well as a thread::JoinHandle
. The thread::JoinHandle
will be for a spawned thread that will read sequence records from the files in r1
and r2
and transform these reads in accordance with the FragmentRegexDesc
provided as geo_re
.
The transformed records are then written out to the fifos given in the FifoXFormData
struct.
Currently, all output is written in FASTA
format, so any quality lines or comment lines
(if the input is FASTQ
) will be dropped. If an error occurs up to the creation of the
spawned thread, then this function returns an Err(anyhow::Error)
. The spawned thread
itself returns a Result<()>
.