[Debian-med-packaging] Bug#1118526: tests: kallistro: corrupted size vs. prev_size

[Tj]

Source: kallisto
Followup-For: Bug #1118526
X-Debbugs-Cc: tj.iam.tj at proton.me

Single-stepping got to the abort point:

3828            cout << "CompactedDBG::construct(): Before split: " << unitigsBefore << " unitigs" << endl;
(gdb) n
CompactedDBG::construct(): Before split: 41 unitigs
3829            cout << "CompactedDBG::construct(): After split (1/" << (reference_mode ? "1" : "2" ) << "): " << unitigsAfter1 << " unitigs" <<  endl;
(gdb) n
CompactedDBG::construct(): After split (1/1): 26 unitigs
3831            cout << "CompactedDBG::construct(): Unitigs split: " << unitigSplit.first << endl;
(gdb) n
CompactedDBG::construct(): Unitigs split: 0
3832            cout << "CompactedDBG::construct(): Unitigs deleted: " << unitigSplit.second << endl;
(gdb) n
CompactedDBG::construct(): Unitigs deleted: 15
3834            cout << endl << "CompactedDBG::construct(): Joining unitigs" << endl;
(gdb) n

CompactedDBG::construct(): Joining unitigs
CompactedDBG<void, void>::construct (this=this at entry=0x7fffffff9140, opt=..., bf=..., r=..., nb_unique_minimizers=nb_unique_minimizers at entry=22, nb_non_unique_minimizers=<optimized out>) at ./ext/bifrost/src/KmerHashTable.hpp:170
170         inline size_t size() const {
(gdb) n
CompactedDBG<void, void>::construct (this=this at entry=0x7fffffff9140, opt=..., bf=..., r=..., nb_unique_minimizers=nb_unique_minimizers at entry=22, nb_non_unique_minimizers=<optimized out>) at ./ext/bifrost/src/CompactedDBG.tcc:3839
3839        const int unitigsAfter3 = size();
(gdb) n
3843            cout << "CompactedDBG::construct(): After join: " << unitigsAfter3 << " unitigs" << endl;
(gdb) n
3839        const int unitigsAfter3 = size();
(gdb) n
3843            cout << "CompactedDBG::construct(): After join: " << unitigsAfter3 << " unitigs" << endl;
(gdb) n
CompactedDBG::construct(): After join: 26 unitigs
3844            cout << "CompactedDBG::construct(): Joined " << joined << " unitigs" << endl;
(gdb) n
CompactedDBG::construct(): Joined 0 unitigs
3862    }
(gdb) n
CompactedDBG<void, void>::construct (this=this at entry=0x7fffffff9140, opt=..., bf=..., r=..., nb_unique_minimizers=nb_unique_minimizers at entry=22, nb_non_unique_minimizers=<optimized out>) at /usr/include/c++/15/bits/new_allocator.h:104
104           ~__new_allocator() _GLIBCXX_USE_NOEXCEPT { }
(gdb) n
CompactedDBG<void, void>::build (this=this at entry=0x7fffffff9140, opt=...) at ./ext/bifrost/src/CompactedDBG.tcc:709
709                     r.clear();
(gdb) n
711             }
(gdb) n
corrupted size vs. prev_size

Thread 1 "kallisto" received signal SIGABRT, Aborted.