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github.com/AndreaGuarracino/paf2chain @v0.1.1
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● updated 14mo agov0.1.1 · 2024-03-27★ 36
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README
paf2chain
convert PAF format to CHAIN format
citation
installation
paf2chain is built with rust, and so we install using cargo:
https://github.com/AndreaGuarracino/paf2chain
cd paf2chain
cargo install --force --path .
usage
Generate alignments with the cigar string attached to the cg:Z: tag.
These can be made by several aligners, including minimap2 -c, wfmash, or lastz --format=paf:wfmash.
With alignments in aln.paf (or aln.paf.gz if gzip-compressed), we would convert it into a CHAIN format file using this call:
paf2chain -i aln.paf > aln.chain
info
paf2chain performs the reverse operation of chain2paf.
Core symbols most depended-on inside this repo
paf_query
called by 4
src/paf.rs
paf_target
called by 4
src/paf.rs
paf_query_begin
called by 3
src/paf.rs
paf_query_end
called by 3
src/paf.rs
paf_target_begin
called by 3
src/paf.rs
_for_each_line_in_file
called by 3
src/paf.rs
global_query_start
called by 3
src/paf.rs
paf_query_length
called by 2
src/paf.rs
Shape
Languages
Rust100%
Modules by API surface
src/paf.rs21 symbols
src/main.rs1 symbols
For agents
$ claude mcp add paf2chain \
-- python -m otcore.mcp_server <graph>