wget http://hypervolu.me/~erik/vg/yeast-whole-genomes.tar.gz
~/genomes/progressiveCactus/bin/runProgressiveCactus.sh ./yeast_star.txt  ./work ./work/yeast.hal --configFile ./cactus_progressive_config.xml  --maxCpus 20
hal2vg work/yeast.hal  --inMemory >yeast.vg
hal2vg work/yeast.hal  --inMemory --refGenome S288c > yeast-S288c.vg
vg mod -X 32 yeast-S288c.vg | vg ids -s - > yeast-S288c-cs.vg

# try again with config from joel, and proper tree topology
~/genomes/progressiveCactus/bin/runProgressiveCactus.sh ./cerevisiae.txt  ./work2 ./work2/yeast.hal --configFile ./similar_yeast_config.xml --maxCpus 20

hal2vg work2/yeast.hal --noAncestors --rootGenome Anc01 --refGenome S288c --inMemory > work2/yeast_h2v.vg
vg mod -X 32 work2/yeast_h2v.vg | vg ids -s - > work2/cactus_yeast.vg

vg mod $(for i in I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI; do echo "-r SK1.chr${i}"; done) -I work2/cactus_yeast.vg | vg mod -N - > work2/cactus_yeast_drop_SK1.vg &
vg mod $(for i in I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI; do echo "-r S288c.chr${i}"; done) work2/cactus_yeast.vg | vg mod -N - > work2/cactus_yeast_S288c.vg &
vg mod $(for i in I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI; do echo "-r SK1.chr${i}"; done) work2/cactus_yeast.vg | vg mod -N - > work2/cactus_yeast_SK1.vg &

# chromosome at a time
for i in I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI
do
cat cerevisiae_chrom.txt | sed -e "s/CHROM/chr${i}/g" > cerevisiae_chr${i}.txt
~/genomes/progressiveCactus/bin/runProgressiveCactus.sh ./cerevisiae_chr${i}.txt  ./work3_chrom${i} ./work3_chrom${i}/yeast_chrom${i}.hal --configFile ./similar_yeast_config.xml --maxCpus 20
done

for i in I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI
do
hal2vg work3_chrom${i}/yeast_chrom${i}.hal  --noAncestors --rootGenome Anc01 --refGenome S288c --inMemory > work3_chrom${i}/yeast_chrom${i}_c2v.vg
vg mod -X 32 work3_chrom${i}/yeast_chrom${i}_c2v.vg | vg ids -s - > work3_chrom${i}/cactus_yeast_chrom${i}.vg
vg mod -r SK1.chr${i} -I work3_chrom${i}/cactus_yeast_chrom${i}.vg | vg mod -N - > work3_chrom${i}/cactus_yeast_drop_SK1_chrom${i}.vg
vg mod -r S288c.chr${i} work3_chrom${i}/cactus_yeast_chrom${i}.vg | vg mod -N - > work3_chrom${i}/cactus_yeast_S288c_chrom${i}.vg
vg mod -r SK1.chr${i} work3_chrom${i}/cactus_yeast_chrom${i}.vg | vg mod -N - > work3_chrom${i}/cactus_yeast_SK1_chrom${i}.vg
done

vg ids -j $(for i in I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI; do echo work3_chrom${i}/cactus_yeast_chrom${i}.vg; done)