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We now provide a script to build a portable precompiled binary as another option to run pandora easily. The portable binary is now provided with the release;
pandora can now provide a meaningful stack trace in case of errors, to facilitate debugging (need to pass flag -DPRINT_STACKTRACE to CMake). Due to this, we now add debug symbols (-g flag) to every pandora build type, but this does not impact performance. The precompiled binary has this enabled.
Changed
We now use the Hunter package manager, removing the requirement of having ZLIB and Boost system-wide installations;
GATB is now a git submodule instead of an external project downloaded and compiled during compilation time. This means that when
git cloning pandora, cgranges and GATB are also downloaded/cloned, and when preparing the build (running cmake), Hunter downloads and installs Boost, GTest and ZLIB. Thus we still need internet connection to prepare the build (running cmake)
but not for compiling (running make).
We now use a GATB fork that accepts a ZLIB custom installation;
Refactored all thirdparty libraries (cgranges, GATB, backward, CLI11, inthash) into their own directory thirdparty.
Fixed
Refactored asserts into exceptions, and now pandora can be compiled correctly in the Release mode. The build process is thus able to create a more optimized binary, resulting in improved performance.
Don't assume Nanopore reads are longer than loci [#265]