Fix splitsequence soft-link mode crash with profile DBs#7
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splitsequence --sequence-split-mode 1 (soft-link) wrote position-based
offsets directly as byte offsets into the index. This is correct for
sequence DBs (1 byte per position) but wrong for profile DBs where each
position occupies PROFILE_READIN_SIZE (27) bytes.
When blastdigp.sh runs iterative search on a long query (>10000nt),
extractqueryprofiles produces a dinucleotide profile and splitsequence
splits it in soft-link mode. The resulting index entries pointed to
misaligned byte offsets (e.g. byte 10000 instead of 10000*27=270000),
causing ungappedprefilter to read garbage profile data and segfault in
Sequence::mapProfile.
The bug was latent because the conditions rarely coincided:
- Target DBs use hard-copy mode (--sequence-split-mode 0), unaffected
- Query profiles only get split when the query exceeds maxSeqLen
- Only the pskvins nucleotide pipeline creates profile DBs that pass
through splitsequence soft-link mode
Fix: multiply startPos and len by PROFILE_READIN_SIZE when writing
soft-link index entries for profile DBs.
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splitsequence --sequence-split-mode 1 (soft-link) wrote position-based offsets directly as byte offsets into the index. This is correct for sequence DBs (1 byte per position) but wrong for profile DBs where each position occupies PROFILE_READIN_SIZE (27) bytes.
When blastdigp.sh runs iterative search on a long query (>10000nt), extractqueryprofiles produces a dinucleotide profile and splitsequence splits it in soft-link mode. The resulting index entries pointed to misaligned byte offsets (e.g. byte 10000 instead of 10000*27=270000), causing ungappedprefilter to read garbage profile data and segfault in Sequence::mapProfile.
The bug was latent because the conditions rarely coincided:
Fix: multiply startPos and len by PROFILE_READIN_SIZE when writing soft-link index entries for profile DBs.