fix: validate integer fields in SamParser to prevent silent atoi() corruption#51
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ZaGrayWolf wants to merge 3 commits intocompiler-research:developfrom
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Mar 28, 2026
| bool SamParser::ParseLine(char* line, SamRecord& record) { | ||
| int field_num = 0; | ||
| char* token = strtok(line, "\t"); | ||
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Please undo all whitespace changes.
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Done. Removed trailing whitespace from blank lines in the amended commit. Added 6 regression tests via ParseFile() (since ParseLine is private), all 16 tests pass including the 6 new ones.
- Add ParseInt() helper using strtol(): validates numeric input, logs warning to std::cerr with field name and line number, returns false to skip malformed record - Replace atoi() calls for flag (field 1), pos (field 3), mapq (field 4), pnext (field 7), tlen (field 8) - Malformed records are now skipped with a diagnostic message instead of being silently written as zero-valued integers - Update .gitignore to exclude reference genome files and large data files Fixes compiler-research#22, closes compiler-research#26
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Six tests via ParseFile() covering all five integer fields (flag, pos, mapq, pnext, tlen) for malformed input and one valid record check. Also fix CMakeLists.txt keyword mixing and ROOT 6.38 namespace in SamToNTuple.cxx (pre-existing build breaks, not related to PR logic). Closes compiler-research#26
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Fixes #22, closes #26
Problem
SamParser::ParseLine()usesatoi()for five integer fields: flag (field 1),pos (field 3), mapq (field 4), pnext (field 7), tlen (field 8).
atoi()returns0 silently on non-numeric input — malformed SAM records are written as
zero-valued integers with no warning, corrupting the output RNTuple.
Fix
ParseInt()helper usingstrtol()for proper validationstd::cerridentifying the field name and line numberfalseto skip the malformed record entirelyatoi()calls inParseLine()Tests
Existing test suite passes (3/3). Regression tests for malformed input
to be added in a follow-up commit.
Status
Draft — opening for early review and CI validation.