"AssertionError: String length does not match CIGAR" when running methratio.py

[grasscarp]

Hi, I got this error when I run methratio.py to parse bam file:

[methratio] @mon Oct 10 11:52:28 2022 Using 90% of available memory (866 MB) as limit
[methratio] @mon Oct 10 11:52:28 2022 Presorting inputs
[methratio] @mon Oct 10 11:52:29 2022 Calling samtools sort on SRR800059.uniq.bam and using 36 MB of memory
[bam_sort_core] merging from 792 files and 24 in-memory blocks...
[methratio] @mon Oct 10 12:04:41 2022 Processing 1 chromosomes at a time
[methratio] @mon Oct 10 12:04:43 2022 Reading CM002885.2 from SRR800059.uniq.tmpSrt.bam with samtools
Traceback (most recent call last):
File "methratio.py", line 588, in
main()
File "methratio.py", line 143, in main
ret = map(chromWorker, argList)
File "methratio.py", line 293, in chromWorker
options.rm_dup, options.trim_fillin, coverage, chromSize)
File "methratio.py", line 467, in get_sam_alignment
seq = parseCigar(seq, cigar)
File "methratio.py", line 457, in parseCigar
assert originalLen == index, "String length does not match CIGAR"
AssertionError: String length does not match CIGAR

---

So I checked the script and I find this function (line 432 - 458):

def parseCigar(seq, cigar):
'''
Delete insertions and dash "-" deletions
>>> parseCigar('ACTAGAATGGCT','3M1I3M1D5M')
'ACTGAA-TGGCT'
>>> parseCigar('ACTG','2M')
Traceback (most recent call last):
...
AssertionError: String length does not match CIGAR
'''
index = 0 # index in seq
originalLen = len(seq)
cigarMatch = cigarRE.findall(cigar)
for align in cigarMatch:
length = int(align[:-1])
op = align[-1]
if op == 'M':
index += length
elif op == 'I':
seq = seq[:index]+seq[index+length:]
elif op == 'D':
seq = seq[:index]+'-'*length+seq[index:]
index += length
else:
raise ValueError("%c not a valid CIGAR character"%(op))
assert originalLen == index, "String length does not match CIGAR"
return seq

Where I felt a little strange about "assert originalLen == index". In my understanding, "index" == "M" number + "D" number, rather than "M" number + "I" number (i.e. "originalLen"). So, "originalLen" won't equal to "index" unless the "I" number equal to the "D" number.
Is this a BUG, or have I misunderstood?