Huffman tree based compression algorithm for SNP data.
Input: .bam file
Usage: -in (input .bam file name) -snp (number of snps) -ind (number of individuals)
Options:
-maf_min -maf_max: minimum and maximum threshold of Minor Allele Frequency for SNPs, that will be included into analysis
-cor Usage of correlation between adjacent snps (0 - do not use correlation, 1 - use correlation)
Output:
"Huffman_result.txt" file will include information of compressed snps: number of correlated snps, frequencies of genotypes, used in Huffman algorithm, optimal number of genotypes in block, final length of encoded string.
"Huffman_ind_result.txt" file will include information about individuals: number of individual, bite cost of individual