Added the handling of haplotype phasing information, now the command should look like this:
simON_reads.py -i ref.fa -n 3000 --enable_homopolymer_error --enable_sequencing_error -snp "locus1:222:C>G:0,locus1:279:C>T:1,locus2:23:G>A:1,locus2:534:C>G:0" > individual1.fastq