ctSkennerton/crass — Issue #35: Seg fault for JCVI_SMPL_1103283000005.fa
Author: ctSkennerton
Created: 2012-02-19 10:08:59+00:00
State: open

```==6066== Memcheck, a memory error detector
==6066== Copyright (C) 2002-2009, and GNU GPL'd, by Julian Seward et al.
==6066== Using Valgrind-3.6.0.SVN-Debian and LibVEX; rerun with -h for copyright info
==6066== Command: crass -o killme -l 4 -k 10 -K 9 JCVI_SMPL_1103283000005.fa
==6066==
[crass_longReadFinder]: Processed 100000
[crass_longReadFinder]: Processed 142352
[crass_singletonFinder]: Processed 100000
[crass_singletonFinder]: Processed 142352
[crass_clusterCore]: 4338 variants mapped to 3664 clusters
==6066== Invalid read of size 1
==6066== at 0x444D67: smithWaterman(std::string&, std::string&, int*, int*, int, int, double) (SmithWaterman.cpp:201)
==6066== by 0x43EAE4: ReadHolder::updateStartStops(int, std::string*, options const*) (ReadHolder.cpp:304)
==6066== by 0x431D33: WorkHorse::parseGroupedDRs(int, std::vector >*, std::vector >*, int*) (WorkHorse.cpp:1657)
==6066== by 0x4360DD: WorkHorse::mungeDRs() (WorkHorse.cpp:537)
==6066== by 0x436921: WorkHorse::parseSeqFiles(std::vector >) (WorkHorse.cpp:362)
==6066== by 0x43A4D2: WorkHorse::doWork(std::vector >) (WorkHorse.cpp:164)
==6066== by 0x40AF4B: main (crass.cpp:553)
==6066== Address 0xc3b0515 is 0 bytes after a block of size 1,061 alloc'd
==6066== at 0x4C27CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
==6066== by 0x731ED98: std::string::_Rep::_S_create(unsigned long, unsigned long, std::allocator const&) (in /usr/lib/libstdc++.so.6.0.13)
==6066== by 0x731F8B4: ??? (in /usr/lib/libstdc++.so.6.0.13)
==6066== by 0x731FA52: std::basic_string, std::allocator >::basic_string(char const*, std::allocator const&) (in /usr/lib/libstdc++.so.6.0.13)
==6066== by 0x40F245: reverseComplement(std::string) (SeqUtils.cpp:81)
==6066== by 0x43E879: ReadHolder::reverseComplementSeq() (ReadHolder.cpp:446)
==6066== by 0x42B748: WorkHorse::populateCoverageArray(std::string, int, std::map, std::allocator > >*, int*, int*, std::vector >*, std::vector >*, int**, int*, bool*, int*, bool*, int*) (WorkHorse.cpp:768)
==6066== by 0x42F85B: WorkHorse::parseGroupedDRs(int, std::vector >*, std::vector >*, int*) (WorkHorse.cpp:1224)
==6066== by 0x4360DD: WorkHorse::mungeDRs() (WorkHorse.cpp:537)
==6066== by 0x436921: WorkHorse::parseSeqFiles(std::vector >) (WorkHorse.cpp:362)
==6066== by 0x43A4D2: WorkHorse::doWork(std::vector >) (WorkHorse.cpp:164)
==6066== by 0x40AF4B: main (crass.cpp:553)
==6066==
==6066== Conditional jump or move depends on uninitialised value(s)
==6066== at 0x444DBC: smithWaterman(std::string&, std::string&, int*, int*, int, int, double) (SmithWaterman.cpp:201)
==6066== by 0x43EAE4: ReadHolder::updateStartStops(int, std::string*, options const*) (ReadHolder.cpp:304)
==6066== by 0x431D33: WorkHorse::parseGroupedDRs(int, std::vector >*, std::vector >*, int*) (WorkHorse.cpp:1657)
==6066== by 0x4360DD: WorkHorse::mungeDRs() (WorkHorse.cpp:537)
==6066== by 0x436921: WorkHorse::parseSeqFiles(std::vector >) (WorkHorse.cpp:362)
==6066== by 0x43A4D2: WorkHorse::doWork(std::vector >) (WorkHorse.cpp:164)
==6066== by 0x40AF4B: main (crass.cpp:553)
==6066== Uninitialised value was created by a heap allocation
==6066== at 0x4C27CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
==6066== by 0x731ED98: std::string::_Rep::_S_create(unsigned long, unsigned long, std::allocator const&) (in /usr/lib/libstdc++.so.6.0.13)
==6066== by 0x731F8B4: ??? (in /usr/lib/libstdc++.so.6.0.13)
==6066== by 0x731FA52: std::basic_string, std::allocator >::basic_string(char const*, std::allocator const&) (in /usr/lib/libstdc++.so.6.0.13)
==6066== by 0x4343C8: WorkHorse::clusterDRReads(int, int*, std::map, std::allocator > >*, std::map, std::allocator > >*, std::less, std::allocator, std::allocator > >*> > >*) (WorkHorse.cpp:1877)
==6066== by 0x435585: WorkHorse::mungeDRs() (WorkHorse.cpp:496)
==6066== by 0x436921: WorkHorse::parseSeqFiles(std::vector >) (WorkHorse.cpp:362)
==6066== by 0x43A4D2: WorkHorse::doWork(std::vector >) (WorkHorse.cpp:164)
==6066== by 0x40AF4B: main (crass.cpp:553)
==6066==
==6066== Conditional jump or move depends on uninitialised value(s)
==6066== at 0x42E405: WorkHorse::calculateDRConsensus(std::map, std::allocator > >*, int*, std::map, std::allocator > >*, std::map, std::allocator > >*, int*, int*, int**, char*, float*, std::vector >*, int*) (WorkHorse.cpp:1069)
==6066== by 0x42F963: WorkHorse::parseGroupedDRs(int, std::vector >*, std::vector >*, int*) (WorkHorse.cpp:1233)
==6066== by 0x4360DD: WorkHorse::mungeDRs() (WorkHorse.cpp:537)
==6066== by 0x436921: WorkHorse::parseSeqFiles(std::vector >) (WorkHorse.cpp:362)
==6066== by 0x43A4D2: WorkHorse::doWork(std::vector >) (WorkHorse.cpp:164)
==6066== by 0x40AF4B: main (crass.cpp:553)
==6066== Uninitialised value was created by a stack allocation
==6066== at 0x4353CA: WorkHorse::mungeDRs() (WorkHorse.cpp:481)
==6066==
==6066== Conditional jump or move depends on uninitialised value(s)
==6066== at 0x42E838: WorkHorse::calculateDRConsensus(std::map, std::allocator > >*, int*, std::map, std::allocator > >*, std::map, std::allocator > >*, int*, int*, int**, char*, float*, std::vector >*, int*) (WorkHorse.cpp:1069)
==6066== by 0x42F963: WorkHorse::parseGroupedDRs(int, std::vector >*, std::vector >*, int*) (WorkHorse.cpp:1233)
==6066== by 0x4360DD: WorkHorse::mungeDRs() (WorkHorse.cpp:537)
==6066== by 0x436921: WorkHorse::parseSeqFiles(std::vector >) (WorkHorse.cpp:362)
==6066== by 0x43A4D2: WorkHorse::doWork(std::vector >) (WorkHorse.cpp:164)
==6066== by 0x40AF4B: main (crass.cpp:553)
==6066== Uninitialised value was created by a stack allocation
==6066== at 0x4353CA: WorkHorse::mungeDRs() (WorkHorse.cpp:481)
==6066==
==6066== Use of uninitialised value of size 8
==6066== at 0x42E900: WorkHorse::calculateDRConsensus(std::map, std::allocator > >*, int*, std::map, std::allocator > >*, std::map, std::allocator > >*, int*, int*, int**, char*, float*, std::vector >*, int*) (WorkHorse.cpp:1072)
==6066== by 0x42F963: WorkHorse::parseGroupedDRs(int, std::vector >*, std::vector >*, int*) (WorkHorse.cpp:1233)
==6066== by 0x4360DD: WorkHorse::mungeDRs() (WorkHorse.cpp:537)
==6066== by 0x436921: WorkHorse::parseSeqFiles(std::vector >) (WorkHorse.cpp:362)
==6066== by 0x43A4D2: WorkHorse::doWork(std::vector >) (WorkHorse.cpp:164)
==6066== by 0x40AF4B: main (crass.cpp:553)
==6066== Uninitialised value was created by a stack allocation
==6066== at 0x4353CA: WorkHorse::mungeDRs() (WorkHorse.cpp:481)
==6066==
==6066== Conditional jump or move depends on uninitialised value(s)
==6066== at 0x42EA10: WorkHorse::calculateDRConsensus(std::map, std::allocator > >*, int*, std::map, std::allocator > >*, std::map, std::allocator > >*, int*, int*, int**, char*, float*, std::vector >*, int*) (WorkHorse.cpp:1089)
==6066== by 0x42F963: WorkHorse::parseGroupedDRs(int, std::vector >*, std::vector >*, int*) (WorkHorse.cpp:1233)
==6066== by 0x4360DD: WorkHorse::mungeDRs() (WorkHorse.cpp:537)
==6066== by 0x436921: WorkHorse::parseSeqFiles(std::vector >) (WorkHorse.cpp:362)
==6066== by 0x43A4D2: WorkHorse::doWork(std::vector >) (WorkHorse.cpp:164)
==6066== by 0x40AF4B: main (crass.cpp:553)
==6066== Uninitialised value was created by a stack allocation
==6066== at 0x4353CA: WorkHorse::mungeDRs() (WorkHorse.cpp:481)
==6066==
==6066== Conditional jump or move depends on uninitialised value(s)
==6066== at 0x42EA2A: WorkHorse::calculateDRConsensus(std::map, std::allocator > >*, int*, std::map, std::allocator > >*, std::map, std::allocator > >*, int*, int*, int**, char*, float*, std::vector >*, int*) (WorkHorse.cpp:1093)
==6066== by 0x42F963: WorkHorse::parseGroupedDRs(int, std::vector >*, std::vector >*, int*) (WorkHorse.cpp:1233)
==6066== by 0x4360DD: WorkHorse::mungeDRs() (WorkHorse.cpp:537)
==6066== by 0x436921: WorkHorse::parseSeqFiles(std::vector >) (WorkHorse.cpp:362)
==6066== by 0x43A4D2: WorkHorse::doWork(std::vector >) (WorkHorse.cpp:164)
==6066== by 0x40AF4B: main (crass.cpp:553)
==6066== Uninitialised value was created by a stack allocation
==6066== at 0x4353CA: WorkHorse::mungeDRs() (WorkHorse.cpp:481)
==6066==
==6066== Invalid read of size 4
==6066== at 0x42AEC6: WorkHorse::populateCoverageArray(std::string, int, std::map, std::allocator > >*, int*, int*, std::vector >*, std::vector >*, int**, int*, bool*, int*, bool*, int*) (WorkHorse.cpp:702)
==6066== by 0x42F85B: WorkHorse::parseGroupedDRs(int, std::vector >*, std::vector >*, int*) (WorkHorse.cpp:1224)
==6066== by 0x4360DD: WorkHorse::mungeDRs() (WorkHorse.cpp:537)
==6066== by 0x436921: WorkHorse::parseSeqFiles(std::vector >) (WorkHorse.cpp:362)
==6066== by 0x43A4D2: WorkHorse::doWork(std::vector >) (WorkHorse.cpp:164)
==6066== by 0x40AF4B: main (crass.cpp:553)
==6066== Address 0xd79d574 is not stack'd, malloc'd or (recently) free'd
==6066==
--6066-- VALGRIND INTERNAL ERROR: Valgrind received a signal 11 (SIGSEGV) - exiting
--6066-- si_code=1; Faulting address: 0x10D608968; sp: 0x40928be60
```