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License: MIT License

Makefile 0.68% C++ 99.03% Shell 0.29%

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jervenbolleman hakon-jon adamnovak zihua ekg schaudge jeizenga huangzhibo kaiyin77 ruixincai

gbwt's Issues

[feature request] document counting

In PrivVG project, document frequencies will be necessary in order to satisfy the differential privacy definition (a single new document might inflate counts a lot if it visits the same edge many times). While FastLocate is good enough for initial prototyping, it won't scale well.

I noticed there's support for that in GCSA2 (SadaCount/SadaSparse), can we please have that in GBWT as well? (cc: @ekg)

Compilation fails on CentOS using GCC 8.3.1

I tried to build on our crimson server (which runs on CentOS), but I'm getting compilation failures on the GBWT. I couldn't tell what was causing the failure myself though--it looks correct to me. Here's the error output:

gbwt.cpp:51:1: error: no declaration matches ‘gbwt::GBWT::GBWT(const gbwt::DynamicGBWT&)’
 GBWT::GBWT(const DynamicGBWT& source) :
 ^~~~
In file included from gbwt.cpp:26:
/private/home/jeizenga/GitHub/vg/include/gbwt/gbwt.h:56:12: note: candidates are: ‘gbwt::GBWT::GBWT(const std::vector<gbwt::GBWT>&)’
   explicit GBWT(const std::vector<GBWT>& sources);
            ^~~~
/private/home/jeizenga/GitHub/vg/include/gbwt/gbwt.h:51:3: note:                 ‘gbwt::GBWT::GBWT(gbwt::GBWT&&)’
   GBWT(GBWT&& source);
   ^~~~
gbwt.cpp:46:1: note:                 ‘gbwt::GBWT::GBWT(const gbwt::GBWT&)’
 GBWT::GBWT(const GBWT& source)
 ^~~~
gbwt.cpp:42:1: note:                 ‘gbwt::GBWT::GBWT()’
 GBWT::GBWT()
 ^~~~
In file included from gbwt.cpp:26:
/private/home/jeizenga/GitHub/vg/include/gbwt/gbwt.h:42:7: note: ‘class gbwt::GBWT’ defined here
 class GBWT
       ^~~~
gbwt.cpp: In member function ‘void gbwt::GBWT::swap(gbwt::GBWT&)’:
gbwt.cpp:77:28: error: ‘struct gbwt::DecompressedRecord’ has no member named ‘swap’
     this->endmarker_record.swap(another.endmarker_record);
                            ^~~~
gbwt.cpp: At global scope:
gbwt.cpp:89:1: error: no declaration matches ‘gbwt::GBWT& gbwt::GBWT::operator=(const gbwt::DynamicGBWT&)’
 GBWT::operator=(const DynamicGBWT& source)
 ^~~~
In file included from gbwt.cpp:26:
/private/home/jeizenga/GitHub/vg/include/gbwt/gbwt.h:60:9: note: candidates are: ‘gbwt::GBWT& gbwt::GBWT::operator=(gbwt::GBWT&&)’
   GBWT& operator=(GBWT&& source);
         ^~~~~~~~
gbwt.cpp:82:1: note:                 ‘gbwt::GBWT& gbwt::GBWT::operator=(const gbwt::GBWT&)’
 GBWT::operator=(const GBWT& source)
 ^~~~
In file included from gbwt.cpp:26:
/private/home/jeizenga/GitHub/vg/include/gbwt/gbwt.h:42:7: note: ‘class gbwt::GBWT’ defined here
 class GBWT
       ^~~~
make: *** [gbwt.o] Error 1

And the compiler info:

-bash-4.2$ c++ --version
c++ (GCC) 8.3.1 20190311 (Red Hat 8.3.1-3)
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

tests fail

Hello,

I'm packaging gbwt for Debian; thank you for your contribution to open source scientific software.

One of the tests fail. Can you give us some advice?

$ uname -a
Linux mrcdev 4.18.0-2-amd64 #1 SMP Debian 4.18.10-2 (2018-11-02) x86_64 GNU/Linux
mcrusoe@mrcdev:~/debian/gbwt$ gcc --version
gcc (Debian 8.2.0-12) 8.2.0

[----------] 6 tests from BasicHaplotypes/VariantTest
[ RUN      ] BasicHaplotypes/VariantTest.VariantPathsStatistics/0
test_variants: /usr/include/sdsl/int_vector_buffer.hpp:217: sdsl::int_vector_buffer<t_width>& sdsl::int_vector_buffer<t_width>::operator=(sdsl::int_vector_buffer<t_width>&&) [with unsigned char t_width = 8]: Assertion `m_ifile.good()' failed.

The current patches are at https://salsa.debian.org/med-team/gbwt/tree/master/debian/patches

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