This PR adds some basic functionality to cactus-hal2chains
ability to do all-vs-all (could previously only do one-vs-all)
option to output bigChain.bb and bigChain.link.bb as needed for the browser
It also fixes up the terminology. As pointed out by #1273 the --targetGenomes option was backwards with respect to how it's defined in the chain format. The option names are fixed/changed so that --queryGenomes and --targetGenomes refer to what you get in the output.
This script will still be very inefficient for big hal files on clusters (or anwyhwere without file caching), because the hal file will need to be copied to a local job for each pairwise comparison. I think the only work-around is to implement a batching system like in cactus-hal2maf eventually...
This PR adds some basic functionality to
cactus-hal2chainsall-vs-all(could previously only do one-vs-all)It also fixes up the terminology. As pointed out by #1273 the
--targetGenomesoption was backwards with respect to how it's defined in the chain format. The option names are fixed/changed so that--queryGenomesand--targetGenomesrefer to what you get in the output.This script will still be very inefficient for big hal files on clusters (or anwyhwere without file caching), because the hal file will need to be copied to a local job for each pairwise comparison. I think the only work-around is to implement a batching system like in
cactus-hal2mafeventually...