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bugfix for printing alignment #7

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bugfix for printing alignment #7

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10 changes: 6 additions & 4 deletions ssw/alignmentmgr.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -107,6 +107,7 @@ from typing import (
Tuple,
Union,
)
import re

from .alignmenttuple import Alignment

Expand Down Expand Up @@ -379,13 +380,14 @@ cdef class AlignmentMgr:
if cigar_array == NULL:
raise OSError('Memory allocation issue')
j = 0
for i in range(0, len(cigar), 2):
length = int(cigar[i])
letter = ord(cigar[i+1])
cigar_tuples = re.findall(r"(\d+)([A-Za-z])", cigar)
for cigar_tuple in cigar_tuples:
length = int(cigar_tuple[0])
letter = ord(cigar_tuple[1])
cigar_array[j] = to_cigar_int(length, letter)
j += 1
res_align.cigar = cigar_array
res_align.cigarLen = len(cigar)//2
res_align.cigarLen = len(cigar_tuples)
else:
res_align.cigar = NULL

Expand Down