Change -f 4 output. #7
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Use log1pexp(x) instead of log1p(exp(x)) as this results in a slightly faster (5%) binary as log1p() and exp() do not need to be calculated for each x value. +// Return "log(1+exp(x))" evaluated carefully for largish "x". +// This is also called the "softplus": https://en.wikipedia.org/wiki/Rectifier_(neural_networks) +// transformation, being a smooth approximation to "max(0,x)". +// +// See: +// - Martin Maechler (2012) "Accurately Computing log(1 − exp(− |a|))": http://cran.r-project.org/web/packages/Rmpfr/vignettes/log1mexp-note.pdf +// - Julia LegExpFunctions package: https://github.com/JuliaStats/LogExpFunctions.jl/blob/master/src/basicfuns.jl +inline double log1pexp(double x) {
Replace std::bind2nd with lambda to avoid:
warning: 'bind2nd<std::plus<double>, double>' is deprecated [-Wdeprecated-declarations]
when specifying C++11 or greater.
Add braces around all statements (if, else, for, while, ...) for better readability.
Reformat code with clang-format (version 12):
clang-format -style=LLVM -i *.cpp *.hpp
Fix the following errors in cbust.cpp and
remove_overlapping_segments.hpp after reformatting:
error: ‘>>’ should be ‘> >’ within a nested template argument list
Not all clang-format changes are applied (like formating of lines
that print text).
Remove unused functions.
Fix asserts: bg and scores have size 0. So test if the capacity is big enough instead.
Only print sequence name and score for -f 4.
Sort only top X clusters per sequence by score if -t is specified.
Update Makefile to create faster binaries:
- cbust_static:
Compile a static binary with a recent version of gcc and glibc
to run on an old distribution as CentOS7. Resulting binary can
be twice as fast.
- cbust_amd_libm_aocc:
Compile a static binary with AMD math library (compiled with AOCC)
for a slightly faster binary than cbust, or cbust_static.
- cbust_amd_libm_gcc:
Compile a static binary with AMD math library (compiled with GCC)
for a slightly faster binary than cbust, or cbust_static.
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Change -f 4 output as last 2 column were not very useful.
Provide smart log1pexp(x) function to replace calling log1p(exp(x)) unconditionally.
Add new ways to compile faster binaries.
Fix some wrong asserts.
Remove unused functions.
Reformat code and add braces around all statements.