srprism's Introduction

SRPRISM - Single Read Paired Read Indel Substitution Minimizer

Version 3.3.0

For questions regarding SRPRISM, please contact Aleksandr Morgulis ([email protected]) or Richa Agarwala ([email protected])

Linux Compilation

Download current source code for SRPRISM
$ git clone https://github.com/ncbi/SRPRISM

Do following:
$ cd SRPRISM/srprism

To enable support for NGS library, needed to access NCBI SRA archive directly,
please uncomment the following line in the beginning of the top level Makefile
# export USE_SRA = 1
This will trigger automatic download and compilation of the NGS library.
In order to use pre-installed NGS and VDB libraries, uncomment the following
lines in the top level Makefile and change them to point to the relevant paths
# export NGS_PATH =
# export VDB_PATH =

To build SRPRISM application, do
$ make

After successful build, srprism executable can be found in app/ subdirectory.

Windows Compilation

Windows 64-bit version of SRPRISM was tested with MS Visual Studio 2019 and
MS Visual Studio 2019 Community Edition. In order to compile the following
is required:

    - MS Visual Studio 2019 (or Community Edition of it);
    - git with git bash (available here: https://git-scm.com/download/win

To compile:

    - select a work directory (in the following $SRP_HOME is used as a
        full pathname of that directory);
    - start git bash and issue the following commands:
        cd $SRP_HOME
        git clone https://github.com/ncbi/SRPRISM
    - start MS Visual Studio 2019 and open solution: $SRP_HOME\SRPRISM\windows\SRPRISM\SRPRISM.sln
    - select Release/x64 configuration
    - in the "Solution Explorer" pane, right click on the solution and select "build solution" in
      the context menu
    - the final executable SRPRISM.exe will be in $SRP_HOME\SRPRISM\windows\SRPRISM\x64\Release\

Usage

Please see srprism/README file for usage infromation and examples.

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srprism's Issues

SRPRISM 3.0.0 fails to compile with GCC 7

Any ideas how this could be fixed?
It's likely related to the stricter handling of templating code in GCC 7, see https://gcc.gnu.org/gcc-7/porting_to.html .

(trimmed output, only first part included)

g++ -I.. -I../.. -std=c++11 -O3 -Wno-deprecated-declarations -c -o batch.o batch.cpp
In file included from ../srprism/query_store.hpp:50:0,
                 from batch.hpp:50,
                 from batch.cpp:38:
../srprism/query_acct.hpp: In member function ‘int srprism::CQueryAcct_TBase<t_scoring>::MaxErr(srprism::TQNum) const’:
../srprism/query_acct.hpp:118:51: error: expected primary-expression before ‘)’ token
         { return query_info_[qn].MaxErr< paired >(); }
                                                   ^
In file included from batch.hpp:50:0,
                 from batch.cpp:38:
../srprism/query_store.hpp: In instantiation of ‘bool srprism::CQueryStore::AddPairedResult(srprism::TQNum*, srprism::TQNum*, int, srprism::TSeqSize, int, int, int, int, srprism::TSeqSize, int, int, int, int) [with t_scoring = srprism::CDefaultScoringSystem; srprism::TQNum = unsigned int; srprism::TSeqSize = unsigned int]’:
batch.cpp:470:9:   required from ‘size_t srprism::CBatch::IdentifyPairs(srprism::CResult*, size_t, size_t) [with int search_mode = 0; size_t = long unsigned int]’
batch.cpp:600:41:   required from ‘bool srprism::CBatch::CombineUnpairedResults(srprism::CResult*, srprism::CResult*, size_t&, size_t&, size_t&) [with int search_mode = 0; size_t = long unsigned int]’
batch.cpp:1063:65:   required from ‘bool srprism::CBatch::InterProcess() [with int search_mode = 0]’
batch.cpp:216:53:   required from here
../srprism/query_store.hpp:665:40: error: invalid operands of types ‘<unresolved overloaded function type>’ and ‘bool’ to binary ‘operator<’
                 int max_err( qa->MaxErr< true >( qn ) );
                              ~~~~~~~~~~^~~~~~
../srprism/query_store.hpp: In instantiation of ‘bool srprism::CQueryStore::AddPairedResult(srprism::TQNum*, srprism::TQNum*, int, srprism::TSeqSize, int, int, int, int, srprism::TSeqSize, int, int, int, int) [with t_scoring = srprism::CSumErrScoringSystem; srprism::TQNum = unsigned int; srprism::TSeqSize = unsigned int]’:
batch.cpp:470:9:   required from ‘size_t srprism::CBatch::IdentifyPairs(srprism::CResult*, size_t, size_t) [with int search_mode = 2; size_t = long unsigned int]’
batch.cpp:600:41:   required from ‘bool srprism::CBatch::CombineUnpairedResults(srprism::CResult*, srprism::CResult*, size_t&, size_t&, size_t&) [with int search_mode = 2; size_t = long unsigned int]’
batch.cpp:1063:65:   required from ‘bool srprism::CBatch::InterProcess() [with int search_mode = 2]’
batch.cpp:219:53:   required from here
../srprism/query_store.hpp:665:40: error: invalid operands of types ‘<unresolved overloaded function type>’ and ‘bool’ to binary ‘operator<’
../srprism/query_store.hpp: In instantiation of ‘bool srprism::CQueryStore::AddPairedResult(srprism::TQNum*, srprism::TQNum*, int, srprism::TSeqSize, int, int, int, int, srprism::TSeqSize, int, int, int, int) [with t_scoring = srprism::CLenMinusErrScoringSystem; srprism::TQNum = unsigned int; srprism::TSeqSize = unsigned int]’:
batch.cpp:470:9:   required from ‘size_t srprism::CBatch::IdentifyPairs(srprism::CResult*, size_t, size_t) [with int search_mode = 1; size_t = long unsigned int]’
batch.cpp:600:41:   required from ‘bool srprism::CBatch::CombineUnpairedResults(srprism::CResult*, srprism::CResult*, size_t&, size_t&, size_t&) [with int search_mode = 1; size_t = long unsigned int]’
batch.cpp:1063:65:   required from ‘bool srprism::CBatch::InterProcess() [with int search_mode = 1]’
batch.cpp:222:53:   required from here
../srprism/query_store.hpp:665:40: error: invalid operands of types ‘<unresolved overloaded function type>’ and ‘bool’ to binary ‘operator<’
../srprism/query_store.hpp: In instantiation of ‘bool srprism::CQueryStore::AddPairedResult(srprism::TQNum*, srprism::TQNum*, int, srprism::TSeqSize, int, int, int, int, srprism::TSeqSize, int, int, int, int) [with t_scoring = srprism::CWeakScoringSystem; srprism::TQNum = unsigned int; srprism::TSeqSize = unsigned int]’:
batch.cpp:470:9:   required from ‘size_t srprism::CBatch::IdentifyPairs(srprism::CResult*, size_t, size_t) [with int search_mode = 3; size_t = long unsigned int]’
batch.cpp:600:41:   required from ‘bool srprism::CBatch::CombineUnpairedResults(srprism::CResult*, srprism::CResult*, size_t&, size_t&, size_t&) [with int search_mode = 3; size_t = long unsigned int]’
batch.cpp:1063:65:   required from ‘bool srprism::CBatch::InterProcess() [with int search_mode = 3]’
batch.cpp:225:48:   required from here
...

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