Crate seq_geom_xform 

seq_geom_xform

seq_geom_xform is a crate for transforming complex fragment library geometries from single-cell sequencing data into simple fragment library geometries.

Structs

FifoXFormData

The information we get back from an xform function that tells us the relevant information about the transformation taking place

FragmentRegexDesc

SeqPair

XformStats

This struct holds some basic statistics about the transformation of a stream of reads.

Traits

FragmentGeomDescExt

Extension methods for FragmentGeomDesc

Functions

xform_read_pairs_to_fifo

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<()>.

xform_read_pairs_to_file

Given input file paths (possibly multiple sets of files) in r1 and r2, read sequence records from these files and transform them in accordance with the FragmentRegexDesc provided as geo_re. The transformed records are then written out to r1_ofile and r2_ofile. Currently all output is written in FASTA format, so any quality lines or comment lines (if the input is FASTQ) will be dropped.