Fix segfault in NEXUS interleaved format parsing#1985
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The non-interleaved sequence length validation check at nexus.cpp:1304 was incorrectly triggering for interleaved alignments. When processing the second (or subsequent) interleave blocks, totalSitesRead increases as expected, but the check treated this as an error. This caused GetSequenceName(fState.curSpecies) to be called with an invalid index (since curSpecies wraps around in interleaved mode), returning nullptr, which then crashed in Enquote(). Fix: - Skip the non-interleaved validation when fState.interleaved is true - Add null check on GetSequenceName result as defensive measure Fixes veg#1984
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Summary
Fixes a segfault (SIGSEGV) when parsing interleaved NEXUS files generated by R's
write.nexus.data.Root Cause
The non-interleaved sequence length validation check at
nexus.cpp:1304was incorrectly triggering for interleaved alignments. When processing the second interleave block,totalSitesReadincreases (expected behavior for interleaved data), but the validation treated this as an error condition.This caused
GetSequenceName(fState.curSpecies)to be called with an out-of-bounds index (curSpecies wraps around in interleaved mode), returningnullptr, which then crashed in_String::Enquote().Fix
!fState.interleavedto the condition guard so the non-interleaved validation only applies to non-interleaved filesGetSequenceNameresult as a defensive measureTesting
Fixes #1984