MAF tiling

Author: Bansho Masutani [email protected] Email: [email protected]

Desc.

This crate consits of tiling a given reads into a "encoded" version of the read.

Contents

Synopsis

Rust

• annotate_dotplot.rs Input: a contig file and its self-self alignmetn file Output: Dataset for D3.js Requirements: Dataset should be consistent with others. Convert Last's self-alignment into JSON object file. The trivial alignments(self to complete self) and small alignments would be removed.

• encode.rs Input: Alignment, Contig, Read, RepeatAnnotation, output location1, and output location2. Output: None(Some stderr messages) Requirements: None To encode reads into array of units by maf alignment. Information on contigs would be written to output location1, while the encoded reads written to output location2. They are JSON-encoded. Example:

cargo run --release --bin encode -- [maf<MAF>] [contigs<Fasta>] [read<FASTA>] [repeat annotation<JSON>] [output<PATH>] [output2<Path>]

To see more detail about the program, see documentation.

• convert_to_d3_data.rs Input: a contig file and a read file Output: Dataset for D3.js Requirements: Input files shoule be generated by encode.rs Convert the dataset into lightweight representation to visualize.

./scripts

• run_cluster.sh Input:None Output:None Requirement: All the variable in this script must be valid. Run experiment on hx cluster.

ToDo