eds

Program msa2eds-mincard constructs Elastic Degenerate Strings from a multiple sequence alignment in FASTA format. Tested on GCC 15.2.1. You can get this repository and compile the HTSlib and SDSL v3 dependencies with

git clone https://github.com/algbio/eds && cd eds
git submodule update --init --recursive ext/htslib ext/sdsl-lite
(cd ext/htslib && autoreconf -i && ./configure && make -j)

Otherwise, if you install HTSlib some other way (for example from its website), change variables HTSLIB_INCLUDE and HTSLIB_LIB in Makefile. Finally, compile msa2esd-mincard and test it with

make
./msa2eds-mincard test/msa.fa -o test/msa.eds

todo

• handle no valid segmentation
• refactor main file
• compact tries to reduce topology ops
• QC on the edses in chr19 experiment