Skip to content

AlignedSegment.set_tag(): validate Hex values for tag type 'H' #1366

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
Open

AlignedSegment.set_tag(): validate Hex values for tag type 'H' #1366

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
ea9a3f7
AlignedSegment.set_tag(): validate Hex values for tag type 'H'
bentyeh Nov 8, 2025
184b61d
bugfix for previous commit: missing trailing doublequote
bentyeh Nov 8, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 7 additions & 0 deletions pysam/libcalignedsegment.pyx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,7 @@ cdef int NCIGAR_CODES = 10

CIGAR2CODE = dict([y, x] for x, y in enumerate(CODE2CIGAR))
CIGAR_REGEX = re.compile("(\d+)([MIDNSHP=XB])")
HEX_VALUE_REGEX = re.compile(r"([0-9A-F][0-9A-F])*") # from SAM specification

# names for keys in dictionary representation of an AlignedSegment
KEY_NAMES = ["name", "flag", "ref_name", "ref_pos", "map_quality", "cigar",
Expand Down Expand Up @@ -2520,6 +2521,12 @@ cdef class AlignedSegment:
value_ptr = <uint8_t*><char*>value
value_size = len(value)+1
elif typecode == b'H':
# validate Hex values
if not HEX_VALUE_REGEX.fullmatch(value):
raise ValueError(
f"Invalid value {value} for tag {tag.decode()} with value_type 'H': "
f"must match the regular expression {HEX_VALUE_REGEX.pattern}"
)
# Note that hex tags are stored the very same
# way as Z string.s
value = force_bytes(value)
Expand Down