UMI tools in rust

UMI stands for Unique Molecular Identifier.

The goal is reproduce some functionalities from umi-tools especially the extract command.

For example, convert the following read

@VH00666:90:AAAWVCCHV:1:1101:24026:1000
GTCAGTTATAGCGGGCGCGCAAAAAAAAAAAAAAAAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCC
[...]

into:

@VH00666:90:AAAWVCCHV:1:1101:24026:1000_GTCAGT
GCGGGCGCGCAAAAAAAAAAAAAAAAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCC

The UMI was GTCAGT and append to the read name, while being removed from the sequence along with the TATA linker.

TODO

• Record where the TATA is found with stats.pos_linker (HashMap<u32, u32>)
• Read / write compressed FASTQ (https://github.com/wckdouglas/fq-filter-reads/)
• Use multithreading