def scheme6(kmer):
'''
3 bit alphabet, MTF, shitty huffman encoding, 0 => 1, 1 => 01, 2 => 000, 3 => 0011, 4 => 0010
modified MTF to not push to front when base is N
'''
def huff_size(c):
return { 0: 1,
1: 2,
2: 3,
3: 4,
4: 4,
}[c]
trans_kmer = mtf.mtf_n(kmer)
size = 0
i = 0
while i < len(trans_kmer):
size += huff_size(trans_kmer[i])
i += 1
return size
def scheme5(kmer):
'''
3 bit alphabet, BWT, MTF, shitty huffman encoding, 0 => 1, 1 => 01, 2 => 000, 3 => 0011, 4 => 0010
Add 6 bits for eol position
modified MTF to not push to front when base is N
'''
def huff_size(c):
return { 0: 1,
1: 2,
2: 3,
3: 4,
4: 4,
}[c]
trans_kmer, eol_idx = bwt.eol_format(bwt.bwt(kmer))
trans_kmer = mtf.mtf_n(trans_kmer)
size = 0
size += 6
i = 0
while i < len(trans_kmer):
size += huff_size(trans_kmer[i])
i += 1
return size
