def scheme1(kmer):
'''
BWT, EOL, 2 bit alphabet
Encoding scheme =
encoding := eol_pos bases
eol_pos := 6 bits for eol, suitable for k <=~ 63
bases := 2 bits for base, 1 bit for RLE, 1 bit for len 2-3, (1 bit for len 2-3 | 6 bits for len <= 63)
Examples: AC == 000 010
AAC == 00100 010
AAAC == 00101 010
AAAAC == 0011000000 010
AAAAAC == 0011000001 010
Three-tiered encoding, run len 1 => 3 bits, run len 2-3 => 5 bits, run len 4-68 => 10 bits
'''
trans_kmer, eol_idx = bwt.eol_format(bwt.bwt(kmer))
size = 0
size += 6
i = 0
while i < len(trans_kmer):
run_length = run_len(trans_kmer, i)
if run_length == 1:
size += 3
elif run_length in [2,3]:
size += 5
else:
size += 10
if run_length > 68:
run_length = 68
i += run_length
return size
def scheme3(kmer):
'''
2 bit alphabet, BWT, MTF, shitty huffman encoding, 0 => 1, 1 => 01, 2 => 000, 3 => 001
Add 6 bits for eol position
'''
def huff_size(c):
return { 0: 1,
1: 2,
2: 3,
3: 3,
}[c]
trans_kmer, eol_idx = bwt.eol_format(bwt.bwt(kmer))
trans_kmer = mtf.mtf(trans_kmer)
size = 0
size += 6
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
