J
Okay danke SeppJ, habe das Programm direkt mal so aufgerufen wie von dir vorgeschlagen. Ich muss nun mal schauen, wie ich bei dieser Seqan-Sache vorgehen soll, denn die Klasse ist nicht von mir, soll aber eingesetzt werden - was würdet ihr da tun?
BTW: hier ist einfach mal der Output was mir SeppJ's Aufrufvariante einbrachte, ich werde dann noch schauen, was ich selbst damit anfangen kann:
joba@joba-laptop:~/Desktop/h2r$ valgrind --tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=20 --track-fds=yes ./h2r --pathtomsa /home/joba/Desktop/h2r/alignments/1JGX_L.fas --msaname 1JGX_L --pathtodesktop /home/joba/Desktop/ --outputdirectory /home/joba/Desktop/h2r/results/
==22987== Memcheck, a memory error detector
==22987== Copyright (C) 2002-2009, and GNU GPL'd, by Julian Seward et al.
==22987== Using Valgrind-3.6.0.SVN-Debian and LibVEX; rerun with -h for copyright info
==22987== Command: ./h2r --pathtomsa /home/joba/Desktop/h2r/alignments/1JGX_L.fas --msaname 1JGX_L --pathtodesktop /home/joba/Desktop/ --outputdirectory /home/joba/Desktop/h2r/results/
==22987==
------------------------------------------------------------------
/ *** Start CPP-Anwendung ***
|
| ***************************************
| * H2r *
| * Version 1.0 15.05.2011 *
| ***************************************
|
| Runtime-Flags:
| --pathtomsa /home/joba/Desktop/h2r/alignments/1JGX_L.fas --msaname 1JGX_L --pathtodesktop /home/joba/Desktop/ --outputdirectory /home/joba/Desktop/h2r/results/
| ... Flags verarbeitet!
| *** START der Berechnung ...
| ... MSA gebildet!
| ... ... Laufzeit: 7.29 Sekunden;
| ... -> MSA-Eigenschaften vor Filter (631 Sequenzen, 281 Spalten);
| ... filtere MSA ...
| ... MSA gefiltert!
| ... -> MSA-Eigenschaften nach Filter (121 Sequenzen, 281 Spalten);
| ... ... Laufzeit: 83.75 Sekunden;
| ... mische MSA und berechne Mixed-MSA ...
| ... MSA gemischt!
| ... ... Laufzeit: 390.98 Sekunden;
| ... gemischtes MSA berechnet!
| ... ... Laufzeit: 1645.59 Sekunden;
| ... ... Laufzeit (nach Sortiervorgang): 1648.05 Sekunden;
| ... schreibe Ergebnisdatei: 'U-Wert-Cutoff;Sequenzahl;WichtigeSpalten;' in Datei;
| *** *** >>> 99. Perzentil der U-Werte: 0.177495; Sequenzen: 121; Spalten: 281
| ---------------------------
| *** ENDE CPP-Anwendung ***
\ ---------------------------------------------------------------
==22987==
==22987== FILE DESCRIPTORS: 3 open at exit.
==22987== Open file descriptor 2: /dev/pts/3
==22987== <inherited from parent>
==22987==
==22987== Open file descriptor 1: /dev/pts/3
==22987== <inherited from parent>
==22987==
==22987== Open file descriptor 0: /dev/pts/3
==22987== <inherited from parent>
==22987==
==22987==
==22987== HEAP SUMMARY:
==22987== in use at exit: 262,799 bytes in 1,018 blocks
==22987== total heap usage: 6,366,184 allocs, 6,365,166 frees, 362,902,283 bytes allocated
==22987==
==22987== 109 bytes in 1 blocks are definitely lost in loss record 1 of 5
==22987== at 0x402569A: operator new(unsigned int) (vg_replace_malloc.c:255)
==22987== by 0x806DF14: void seqan::allocate<seqan::String<char, seqan::Alloc<void> >, char, unsigned int, seqan::AllocateStorage_>(seqan::String<char, seqan::Alloc<void> >&, char*&, unsigned int, seqan::Tag<seqan::AllocateStorage_>) (basic_allocator_interface.h:199)
==22987== by 0x806D62C: seqan::Value<seqan::String<char, seqan::Alloc<void> >, 0>::Type* seqan::_allocateStorage<char, void>(seqan::String<char, seqan::Alloc<void> >&, unsigned int) (string_alloc.h:340)
==22987== by 0x806CE66: seqan::Value<seqan::String<char, seqan::Alloc<void> >, 0>::Type* seqan::_reallocateStorage<char, seqan::Alloc<void>, unsigned int>(seqan::String<char, seqan::Alloc<void> >&, unsigned int) (string_base.h:1430)
==22987== by 0x806BC38: seqan::Value<seqan::String<char, seqan::Alloc<void> >, 0>::Type* seqan::_reallocateStorage<char, seqan::Alloc<void>, unsigned int>(seqan::String<char, seqan::Alloc<void> >&, unsigned int, seqan::Tag<seqan::TagGenerous_>) (string_base.h:1483)
==22987== by 0x806C42C: seqan::Size<seqan::String<char, seqan::Alloc<void> > >::Type seqan::ClearSpaceExpandStringBase_<seqan::Tag<seqan::TagGenerous_> const>::_clearSpace_<seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >&, seqan::Size<seqan::String<char, seqan::Alloc<void> > >::Type) (string_base.h:528)
==22987== by 0x806AFFB: seqan::Size<seqan::String<char, seqan::Alloc<void> > >::Type seqan::_clearSpace<char, seqan::Alloc<void>, unsigned int, seqan::TagGenerous_>(seqan::String<char, seqan::Alloc<void> >&, unsigned int, seqan::Tag<seqan::TagGenerous_>) (string_base.h:726)
==22987== by 0x80692DE: void seqan::AssignString_<seqan::Tag<seqan::TagGenerous_> const>::assign_<seqan::String<char, seqan::Alloc<void> >, seqan::String<char, seqan::Alloc<void> > const>(seqan::String<char, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&) (string_base.h:871)
==22987== by 0x8065FAB: void seqan::assign<char, seqan::Alloc<void>, seqan::String<char, seqan::Alloc<void> >, seqan::TagGenerous_>(seqan::String<char, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&, seqan::Tag<seqan::TagGenerous_>) (string_base.h:920)
==22987== by 0x8062FFB: void seqan::assign<char, seqan::Alloc<void>, seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&) (string_base.h:852)
==22987== by 0x8060304: seqan::String<char, seqan::Alloc<void> >::String(seqan::String<char, seqan::Alloc<void> > const&) (string_alloc.h:109)
==22987== by 0x806C047: void seqan::ValueConstructor_::construct<seqan::Iter<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::AdaptorIterator<seqan::String<char, seqan::Alloc<void> >*, seqan::Tag<seqan::Default_> const> >, seqan::String<char, seqan::Alloc<void> > >(seqan::Iter<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::AdaptorIterator<seqan::String<char, seqan::Alloc<void> >*, seqan::Tag<seqan::Default_> const> >, seqan::String<char, seqan::Alloc<void> > const&) (basic_alphabet_interface.h:115)
==22987== by 0x806AD26: void seqan::valueConstruct<seqan::Iter<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::AdaptorIterator<seqan::String<char, seqan::Alloc<void> >*, seqan::Tag<seqan::Default_> const> >, seqan::String<char, seqan::Alloc<void> > >(seqan::Iter<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::AdaptorIterator<seqan::String<char, seqan::Alloc<void> >*, seqan::Tag<seqan::Default_> const> >, seqan::String<char, seqan::Alloc<void> > const&) (basic_alphabet_interface.h:204)
==22987== by 0x8069004: void seqan::AppendValueToString_<seqan::Tag<seqan::TagGenerous_> const>::appendValue_<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::String<char, seqan::Alloc<void> > const>(seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&) (string_base.h:1216)
==22987== by 0x8065DB1: void seqan::appendValue<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void>, seqan::String<char, seqan::Alloc<void> >, seqan::TagGenerous_>(seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&, seqan::Tag<seqan::TagGenerous_>) (string_base.h:1236)
==22987== by 0x8062C7D: void seqan::appendValue<seqan::String<char, seqan::Alloc<void> >, seqan::String<char, seqan::Alloc<void> >, seqan::TagGenerous_>(seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >&, seqan::String<char, seqan::Alloc<void> > const&, seqan::Tag<seqan::TagGenerous_> const&) (string_set_owner.h:132)
==22987== by 0x805F9AF: void seqan::appendValue<seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >, seqan::String<char, seqan::Alloc<void> > >(seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >&, seqan::String<char, seqan::Alloc<void> > const&) (sequence_interface.h:1201)
==22987== by 0x805C7F2: Msa::readMsaFromFile(std::string) (h2r.cpp:247)
==22987== by 0x805C4F4: Msa::Msa(std::string, seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >&, seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >&, std::vector<std::string, std::allocator<std::string> >&, std::vector<std::string, std::allocator<std::string> >&, std::string) (h2r.cpp:203)
==22987== by 0x805ADE5: main (h2r.cpp:3709)
==22987==
==22987== 422 bytes in 1 blocks are definitely lost in loss record 2 of 5
==22987== at 0x402569A: operator new(unsigned int) (vg_replace_malloc.c:255)
==22987== by 0x806DF14: void seqan::allocate<seqan::String<char, seqan::Alloc<void> >, char, unsigned int, seqan::AllocateStorage_>(seqan::String<char, seqan::Alloc<void> >&, char*&, unsigned int, seqan::Tag<seqan::AllocateStorage_>) (basic_allocator_interface.h:199)
==22987== by 0x806D62C: seqan::Value<seqan::String<char, seqan::Alloc<void> >, 0>::Type* seqan::_allocateStorage<char, void>(seqan::String<char, seqan::Alloc<void> >&, unsigned int) (string_alloc.h:340)
==22987== by 0x806CE66: seqan::Value<seqan::String<char, seqan::Alloc<void> >, 0>::Type* seqan::_reallocateStorage<char, seqan::Alloc<void>, unsigned int>(seqan::String<char, seqan::Alloc<void> >&, unsigned int) (string_base.h:1430)
==22987== by 0x806BC38: seqan::Value<seqan::String<char, seqan::Alloc<void> >, 0>::Type* seqan::_reallocateStorage<char, seqan::Alloc<void>, unsigned int>(seqan::String<char, seqan::Alloc<void> >&, unsigned int, seqan::Tag<seqan::TagGenerous_>) (string_base.h:1483)
==22987== by 0x806C42C: seqan::Size<seqan::String<char, seqan::Alloc<void> > >::Type seqan::ClearSpaceExpandStringBase_<seqan::Tag<seqan::TagGenerous_> const>::_clearSpace_<seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >&, seqan::Size<seqan::String<char, seqan::Alloc<void> > >::Type) (string_base.h:528)
==22987== by 0x806AFFB: seqan::Size<seqan::String<char, seqan::Alloc<void> > >::Type seqan::_clearSpace<char, seqan::Alloc<void>, unsigned int, seqan::TagGenerous_>(seqan::String<char, seqan::Alloc<void> >&, unsigned int, seqan::Tag<seqan::TagGenerous_>) (string_base.h:726)
==22987== by 0x80692DE: void seqan::AssignString_<seqan::Tag<seqan::TagGenerous_> const>::assign_<seqan::String<char, seqan::Alloc<void> >, seqan::String<char, seqan::Alloc<void> > const>(seqan::String<char, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&) (string_base.h:871)
==22987== by 0x8065FAB: void seqan::assign<char, seqan::Alloc<void>, seqan::String<char, seqan::Alloc<void> >, seqan::TagGenerous_>(seqan::String<char, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&, seqan::Tag<seqan::TagGenerous_>) (string_base.h:920)
==22987== by 0x8062FFB: void seqan::assign<char, seqan::Alloc<void>, seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&) (string_base.h:852)
==22987== by 0x8060304: seqan::String<char, seqan::Alloc<void> >::String(seqan::String<char, seqan::Alloc<void> > const&) (string_alloc.h:109)
==22987== by 0x806C047: void seqan::ValueConstructor_::construct<seqan::Iter<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::AdaptorIterator<seqan::String<char, seqan::Alloc<void> >*, seqan::Tag<seqan::Default_> const> >, seqan::String<char, seqan::Alloc<void> > >(seqan::Iter<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::AdaptorIterator<seqan::String<char, seqan::Alloc<void> >*, seqan::Tag<seqan::Default_> const> >, seqan::String<char, seqan::Alloc<void> > const&) (basic_alphabet_interface.h:115)
==22987== by 0x806AD26: void seqan::valueConstruct<seqan::Iter<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::AdaptorIterator<seqan::String<char, seqan::Alloc<void> >*, seqan::Tag<seqan::Default_> const> >, seqan::String<char, seqan::Alloc<void> > >(seqan::Iter<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::AdaptorIterator<seqan::String<char, seqan::Alloc<void> >*, seqan::Tag<seqan::Default_> const> >, seqan::String<char, seqan::Alloc<void> > const&) (basic_alphabet_interface.h:204)
==22987== by 0x8069004: void seqan::AppendValueToString_<seqan::Tag<seqan::TagGenerous_> const>::appendValue_<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::String<char, seqan::Alloc<void> > const>(seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&) (string_base.h:1216)
==22987== by 0x8065DB1: void seqan::appendValue<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void>, seqan::String<char, seqan::Alloc<void> >, seqan::TagGenerous_>(seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&, seqan::Tag<seqan::TagGenerous_>) (string_base.h:1236)
==22987== by 0x8062C7D: void seqan::appendValue<seqan::String<char, seqan::Alloc<void> >, seqan::String<char, seqan::Alloc<void> >, seqan::TagGenerous_>(seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >&, seqan::String<char, seqan::Alloc<void> > const&, seqan::Tag<seqan::TagGenerous_> const&) (string_set_owner.h:132)
==22987== by 0x805F9AF: void seqan::appendValue<seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >, seqan::String<char, seqan::Alloc<void> > >(seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >&, seqan::String<char, seqan::Alloc<void> > const&) (sequence_interface.h:1201)
==22987== by 0x805C828: Msa::readMsaFromFile(std::string) (h2r.cpp:249)
==22987== by 0x805C4F4: Msa::Msa(std::string, seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >&, seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >&, std::vector<std::string, std::allocator<std::string> >&, std::vector<std::string, std::allocator<std::string> >&, std::string) (h2r.cpp:203)
==22987== by 0x805ADE5: main (h2r.cpp:3709)
==22987==
==22987== 3,502 bytes in 37 blocks are definitely lost in loss record 3 of 5
==22987== at 0x402569A: operator new(unsigned int) (vg_replace_malloc.c:255)
==22987== by 0x806DF14: void seqan::allocate<seqan::String<char, seqan::Alloc<void> >, char, unsigned int, seqan::AllocateStorage_>(seqan::String<char, seqan::Alloc<void> >&, char*&, unsigned int, seqan::Tag<seqan::AllocateStorage_>) (basic_allocator_interface.h:199)
==22987== by 0x806D62C: seqan::Value<seqan::String<char, seqan::Alloc<void> >, 0>::Type* seqan::_allocateStorage<char, void>(seqan::String<char, seqan::Alloc<void> >&, unsigned int) (string_alloc.h:340)
==22987== by 0x806CE66: seqan::Value<seqan::String<char, seqan::Alloc<void> >, 0>::Type* seqan::_reallocateStorage<char, seqan::Alloc<void>, unsigned int>(seqan::String<char, seqan::Alloc<void> >&, unsigned int) (string_base.h:1430)
==22987== by 0x806BC38: seqan::Value<seqan::String<char, seqan::Alloc<void> >, 0>::Type* seqan::_reallocateStorage<char, seqan::Alloc<void>, unsigned int>(seqan::String<char, seqan::Alloc<void> >&, unsigned int, seqan::Tag<seqan::TagGenerous_>) (string_base.h:1483)
==22987== by 0x806C42C: seqan::Size<seqan::String<char, seqan::Alloc<void> > >::Type seqan::ClearSpaceExpandStringBase_<seqan::Tag<seqan::TagGenerous_> const>::_clearSpace_<seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >&, seqan::Size<seqan::String<char, seqan::Alloc<void> > >::Type) (string_base.h:528)
==22987== by 0x806AFFB: seqan::Size<seqan::String<char, seqan::Alloc<void> > >::Type seqan::_clearSpace<char, seqan::Alloc<void>, unsigned int, seqan::TagGenerous_>(seqan::String<char, seqan::Alloc<void> >&, unsigned int, seqan::Tag<seqan::TagGenerous_>) (string_base.h:726)
==22987== by 0x80692DE: void seqan::AssignString_<seqan::Tag<seqan::TagGenerous_> const>::assign_<seqan::String<char, seqan::Alloc<void> >, seqan::String<char, seqan::Alloc<void> > const>(seqan::String<char, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&) (string_base.h:871)
==22987== by 0x8065FAB: void seqan::assign<char, seqan::Alloc<void>, seqan::String<char, seqan::Alloc<void> >, seqan::TagGenerous_>(seqan::String<char, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&, seqan::Tag<seqan::TagGenerous_>) (string_base.h:920)
==22987== by 0x8062FFB: void seqan::assign<char, seqan::Alloc<void>, seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&) (string_base.h:852)
==22987== by 0x8060304: seqan::String<char, seqan::Alloc<void> >::String(seqan::String<char, seqan::Alloc<void> > const&) (string_alloc.h:109)
==22987== by 0x806C0AE: void seqan::ValueConstructor_::construct<seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> > const&) (basic_alphabet_interface.h:115)
==22987== by 0x806AD6B: void seqan::valueConstruct<seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> > const&) (basic_alphabet_interface.h:204)
==22987== by 0x806909D: void seqan::AppendValueToString_<seqan::Tag<seqan::TagGenerous_> const>::appendValue_<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::String<char, seqan::Alloc<void> > const>(seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&) (string_base.h:1221)
==22987== by 0x8065DB1: void seqan::appendValue<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void>, seqan::String<char, seqan::Alloc<void> >, seqan::TagGenerous_>(seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&, seqan::Tag<seqan::TagGenerous_>) (string_base.h:1236)
==22987== by 0x8062C7D: void seqan::appendValue<seqan::String<char, seqan::Alloc<void> >, seqan::String<char, seqan::Alloc<void> >, seqan::TagGenerous_>(seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >&, seqan::String<char, seqan::Alloc<void> > const&, seqan::Tag<seqan::TagGenerous_> const&) (string_set_owner.h:132)
==22987== by 0x805F9AF: void seqan::appendValue<seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >, seqan::String<char, seqan::Alloc<void> > >(seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >&, seqan::String<char, seqan::Alloc<void> > const&) (sequence_interface.h:1201)
==22987== by 0x805C7F2: Msa::readMsaFromFile(std::string) (h2r.cpp:247)
==22987== by 0x805C4F4: Msa::Msa(std::string, seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >&, seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >&, std::vector<std::string, std::allocator<std::string> >&, std::vector<std::string, std::allocator<std::string> >&, std::string) (h2r.cpp:203)
==22987== by 0x805ADE5: main (h2r.cpp:3709)
==22987==
==22987== 15,614 bytes in 37 blocks are definitely lost in loss record 4 of 5
==22987== at 0x402569A: operator new(unsigned int) (vg_replace_malloc.c:255)
==22987== by 0x806DF14: void seqan::allocate<seqan::String<char, seqan::Alloc<void> >, char, unsigned int, seqan::AllocateStorage_>(seqan::String<char, seqan::Alloc<void> >&, char*&, unsigned int, seqan::Tag<seqan::AllocateStorage_>) (basic_allocator_interface.h:199)
==22987== by 0x806D62C: seqan::Value<seqan::String<char, seqan::Alloc<void> >, 0>::Type* seqan::_allocateStorage<char, void>(seqan::String<char, seqan::Alloc<void> >&, unsigned int) (string_alloc.h:340)
==22987== by 0x806CE66: seqan::Value<seqan::String<char, seqan::Alloc<void> >, 0>::Type* seqan::_reallocateStorage<char, seqan::Alloc<void>, unsigned int>(seqan::String<char, seqan::Alloc<void> >&, unsigned int) (string_base.h:1430)
==22987== by 0x806BC38: seqan::Value<seqan::String<char, seqan::Alloc<void> >, 0>::Type* seqan::_reallocateStorage<char, seqan::Alloc<void>, unsigned int>(seqan::String<char, seqan::Alloc<void> >&, unsigned int, seqan::Tag<seqan::TagGenerous_>) (string_base.h:1483)
==22987== by 0x806C42C: seqan::Size<seqan::String<char, seqan::Alloc<void> > >::Type seqan::ClearSpaceExpandStringBase_<seqan::Tag<seqan::TagGenerous_> const>::_clearSpace_<seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >&, seqan::Size<seqan::String<char, seqan::Alloc<void> > >::Type) (string_base.h:528)
==22987== by 0x806AFFB: seqan::Size<seqan::String<char, seqan::Alloc<void> > >::Type seqan::_clearSpace<char, seqan::Alloc<void>, unsigned int, seqan::TagGenerous_>(seqan::String<char, seqan::Alloc<void> >&, unsigned int, seqan::Tag<seqan::TagGenerous_>) (string_base.h:726)
==22987== by 0x80692DE: void seqan::AssignString_<seqan::Tag<seqan::TagGenerous_> const>::assign_<seqan::String<char, seqan::Alloc<void> >, seqan::String<char, seqan::Alloc<void> > const>(seqan::String<char, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&) (string_base.h:871)
==22987== by 0x8065FAB: void seqan::assign<char, seqan::Alloc<void>, seqan::String<char, seqan::Alloc<void> >, seqan::TagGenerous_>(seqan::String<char, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&, seqan::Tag<seqan::TagGenerous_>) (string_base.h:920)
==22987== by 0x8062FFB: void seqan::assign<char, seqan::Alloc<void>, seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&) (string_base.h:852)
==22987== by 0x8060304: seqan::String<char, seqan::Alloc<void> >::String(seqan::String<char, seqan::Alloc<void> > const&) (string_alloc.h:109)
==22987== by 0x806C0AE: void seqan::ValueConstructor_::construct<seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> > const&) (basic_alphabet_interface.h:115)
==22987== by 0x806AD6B: void seqan::valueConstruct<seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> > const&) (basic_alphabet_interface.h:204)
==22987== by 0x806909D: void seqan::AppendValueToString_<seqan::Tag<seqan::TagGenerous_> const>::appendValue_<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::String<char, seqan::Alloc<void> > const>(seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&) (string_base.h:1221)
==22987== by 0x8065DB1: void seqan::appendValue<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void>, seqan::String<char, seqan::Alloc<void> >, seqan::TagGenerous_>(seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&, seqan::Tag<seqan::TagGenerous_>) (string_base.h:1236)
==22987== by 0x8062C7D: void seqan::appendValue<seqan::String<char, seqan::Alloc<void> >, seqan::String<char, seqan::Alloc<void> >, seqan::TagGenerous_>(seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >&, seqan::String<char, seqan::Alloc<void> > const&, seqan::Tag<seqan::TagGenerous_> const&) (string_set_owner.h:132)
==22987== by 0x805F9AF: void seqan::appendValue<seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >, seqan::String<char, seqan::Alloc<void> > >(seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >&, seqan::String<char, seqan::Alloc<void> > const&) (sequence_interface.h:1201)
==22987== by 0x805C828: Msa::readMsaFromFile(std::string) (h2r.cpp:249)
==22987== by 0x805C4F4: Msa::Msa(std::string, seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >&, seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> const> >&, std::vector<std::string, std::allocator<std::string> >&, std::vector<std::string, std::allocator<std::string> >&, std::string) (h2r.cpp:203)
==22987== by 0x805ADE5: main (h2r.cpp:3709)
==22987==
==22987== 243,152 bytes in 942 blocks are definitely lost in loss record 5 of 5
==22987== at 0x402569A: operator new(unsigned int) (vg_replace_malloc.c:255)
==22987== by 0x806DF14: void seqan::allocate<seqan::String<char, seqan::Alloc<void> >, char, unsigned int, seqan::AllocateStorage_>(seqan::String<char, seqan::Alloc<void> >&, char*&, unsigned int, seqan::Tag<seqan::AllocateStorage_>) (basic_allocator_interface.h:199)
==22987== by 0x806D62C: seqan::Value<seqan::String<char, seqan::Alloc<void> >, 0>::Type* seqan::_allocateStorage<char, void>(seqan::String<char, seqan::Alloc<void> >&, unsigned int) (string_alloc.h:340)
==22987== by 0x806CE66: seqan::Value<seqan::String<char, seqan::Alloc<void> >, 0>::Type* seqan::_reallocateStorage<char, seqan::Alloc<void>, unsigned int>(seqan::String<char, seqan::Alloc<void> >&, unsigned int) (string_base.h:1430)
==22987== by 0x806BC38: seqan::Value<seqan::String<char, seqan::Alloc<void> >, 0>::Type* seqan::_reallocateStorage<char, seqan::Alloc<void>, unsigned int>(seqan::String<char, seqan::Alloc<void> >&, unsigned int, seqan::Tag<seqan::TagGenerous_>) (string_base.h:1483)
==22987== by 0x806C42C: seqan::Size<seqan::String<char, seqan::Alloc<void> > >::Type seqan::ClearSpaceExpandStringBase_<seqan::Tag<seqan::TagGenerous_> const>::_clearSpace_<seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >&, seqan::Size<seqan::String<char, seqan::Alloc<void> > >::Type) (string_base.h:528)
==22987== by 0x806AFFB: seqan::Size<seqan::String<char, seqan::Alloc<void> > >::Type seqan::_clearSpace<char, seqan::Alloc<void>, unsigned int, seqan::TagGenerous_>(seqan::String<char, seqan::Alloc<void> >&, unsigned int, seqan::Tag<seqan::TagGenerous_>) (string_base.h:726)
==22987== by 0x80692DE: void seqan::AssignString_<seqan::Tag<seqan::TagGenerous_> const>::assign_<seqan::String<char, seqan::Alloc<void> >, seqan::String<char, seqan::Alloc<void> > const>(seqan::String<char, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&) (string_base.h:871)
==22987== by 0x8065FAB: void seqan::assign<char, seqan::Alloc<void>, seqan::String<char, seqan::Alloc<void> >, seqan::TagGenerous_>(seqan::String<char, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&, seqan::Tag<seqan::TagGenerous_>) (string_base.h:920)
==22987== by 0x8062FFB: void seqan::assign<char, seqan::Alloc<void>, seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> > const&) (string_base.h:852)
==22987== by 0x8060304: seqan::String<char, seqan::Alloc<void> >::String(seqan::String<char, seqan::Alloc<void> > const&) (string_alloc.h:109)
==22987== by 0x806C0AE: void seqan::ValueConstructor_::construct<seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> > const&) (basic_alphabet_interface.h:115)
==22987== by 0x806AD6B: void seqan::valueConstruct<seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> > const&) (basic_alphabet_interface.h:204)
==22987== by 0x806CF6C: void seqan::_arrayConstructCopyDefault<seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> >*>(seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> >*) (basic_alphabet_interface.h:383)
==22987== by 0x806BDDE: void seqan::_arrayConstructCopyPointer<seqan::String<char, seqan::Alloc<void> >, seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> >*, seqan::False) (basic_alphabet_trait_basic.h:135)
==22987== by 0x806A81C: void seqan::arrayConstructCopy<seqan::String<char, seqan::Alloc<void> >, seqan::String<char, seqan::Alloc<void> > >(seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> >*, seqan::String<char, seqan::Alloc<void> >*) (basic_alphabet_trait_basic.h:144)
==22987== by 0x806C579: void seqan::_reserveStorage<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void>, unsigned int, seqan::TagGenerous_>(seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >&, unsigned int, seqan::Tag<seqan::TagGenerous_>) (string_base.h:1592)
==22987== by 0x806B15C: seqan::Size<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> > >::Type seqan::reserve<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void>, unsigned int, seqan::TagGenerous_>(seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >&, unsigned int, seqan::Tag<seqan::TagGenerous_>) (string_base.h:1611)
==22987== by 0x80695F6: seqan::Size<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> > >::Type seqan::_Resize_String<seqan::Tag<seqan::TagGenerous_> const>::resize_<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> > >(seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >&, seqan::Size<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> > >::Type) (string_base.h:1640)
==22987== by 0x806AC58: seqan::Size<seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> > >::Type seqan::resize<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void>, unsigned int, seqan::TagGenerous_>(seqan::String<seqan::String<char, seqan::Alloc<void> >, seqan::Alloc<void> >&, unsigned int, seqan::Tag<seqan::TagGenerous_>) (string_base.h:1705)
==22987==
==22987== LEAK SUMMARY:
==22987== definitely lost: 262,799 bytes in 1,018 blocks
==22987== indirectly lost: 0 bytes in 0 blocks
==22987== possibly lost: 0 bytes in 0 blocks
==22987== still reachable: 0 bytes in 0 blocks
==22987== suppressed: 0 bytes in 0 blocks
==22987==
==22987== For counts of detected and suppressed errors, rerun with: -v
==22987== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 18 from 7)
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