ParBLiSS kmerind

Kmerind is a library in the Parallel Bioinformatics Library for Short Sequences project (ParBLiSS).

Kmerind provides k-mer indexing capability for biological sequence data.

Please take a look at our Wiki.

Overview

ParBLiSS is a C++ library for distributed and multi-core bioinformatics algorithms. It requires C++ 11 features and MPI (OpenMP not required). The library is implemented as a set of templated classes. As such, most of the code is in header form, and are incorporated into the user code via #include.

K-merind provides basic parallel sequence file access and k-mer index construction and query. Currently, it supports indices for frequency, position, and quality of kmers from short reads and whole genomes, using FASTQ and FASTA formats.

Build

Dependencies

Required:

• c++11 supporting compiler -- g++ (version 4.8.1+ due to "decltype" and other c++11 features) or -- icpc (version 16+ due to constexpr functions and initializers) or -- clang (version 3.5+ - cmake generated make file has problems with prior versions. or 3.7+ if openmp is used)
• cmake (version 2.8+)
• an MPI implementation, one of the following -- openmpi (version 1.7+ due to use of MPI_IN_PLACE) -- mpich2 (version 1.5 +) -- mvapich (tested with version 2.1.7) -- intel mpi library (poorly tested)

See http://en.cppreference.com/w/cpp/compiler_support

Optional libraries are:

boost_log, boost_system, boost_thread, boost_program-options

These are only needed if you intend to turn on boost log engine.

Optional tools include:

• ccmake (for graphical cmake configuration)
• perl, and perl packages Term::ANSIColor, Getopt::ArgvFile, Getopt::Long, Regexp::Common (for g++ error message formatting)

Getting the source

git clone https://github.com/ParBLiSS/kmerind.git
cd kmerind
git submodule init
git submodule update

Configuring for build

mkdir kmerind-build
cd kmerind-build
cmake ../kmerind

alternatively, instead of cmake ../kmerind, you can use

ccmake ../kmerind

CMake Parameters

The following are important parameters:

• CMAKE_BUILD_TYPE: defaults to Release.

• ENABLE_TESTING: On allows BUILD_TEST_APPLICATIONS to show, which enables building the test applications

• BUILD_EXAMPLE_APPLICATION: On allows applications in the examples directory to be built

• LOG_ENGINE: chooses which log engine to use.

• LOGGER_VERBOSITY: chooses the type of messages to prin.

• ENABLE_SANITIZER: turns on g++'s address or thread sanitizer. Use SANITIZER_STYLE to configure. This is for debugging

• ENABLE_STLFILT: turns on g++ error message post processing to make them human readable. Control verbosity via STLFIL_VERBOSITY

It is highly recommended that ccmake be used until you've become familiar with the available CMake options and how to specify them on the commandlinie.

Compiling

make

Important for developers using Intel Compilers, please see the "Intel Compiler Specific Issues" section at the end of the document.

Running the tests

ctest -T Test

or

make test

Building the documentation

make doc

Using Bliss

Please see Wiki.

Configuring Eclipse:

Cmake typically uses a out-of-source build. to generate eclipse compatible .project and .cproject files, supply

-G"Eclipse CDT4 - Unix Makefiles"

to cmake.

Recommend that ptp, egit, and cmake ed also be installed.

Intel Compiler Specific Issues

With Intel C Compiler (icc) version 15, the following compilation error is observed:

Internal error: assertion failed at: "shared/cfe/edgcpfe/il.c", line 18295

While there is very little information to be found on the internet related to this error, we have theorized that this is a compiler bug related to auto type deduction in templated function instantiation. It appears that ICC is unable to auto deduce the data type and size of a statically sized array of the form

datatype x[len]

which as a function parameter is specified as

datatype (&x)[len]

with datatype and len being template parameters for the function.

This error appears only for bitgroup_ops.hpp. Attempts to replicate the error in a separate test code was not successful. The workaround is to fully specify the template parameters for the function so to avoid automatic type deduction in this case.

It is not clear if other function parameter forms also cause this error.