MatchSequences.jl

Grant Billings 5/31/23

Create the package

t = Template(; user="gtbil", authors=["Grant Billings"], plugins=[License(name="MIT"), Git(), GitHubActions(),],)
t("MatchSequences")

This create a folder in C:\Users\grant\.julia\dev\MatchSequences. For getting git working, delete the default .git folder if it exists and copy in the one you get from the following (after authenticating):

gh repo clone gtbil/MatchSequences.jl
# then copy files into the same directory as the project above^

To load the environment in the Julia REPL in VSCode

import Pkg
Pkg.activate("MatchSequences")
# then to close
Pkg.activate()

To memory profile

using Profile
using PProf

Profile.Allocs.clear()

# Profile.Allocs.@profile sample_rate=0.01 main("../CokerTest/Coker312_A01.fasta")
Profile.Allocs.@profile sample_rate=1 MatchSequences.benchmark(t′, sa, l_vec, lms_vec, out_vec, heads, tails,
                               lms_subvec1, lms_subvec2, 
                               lms_boolvec1, lms_boolvec2, numlms; σ_in = col);

PProf.Allocs.pprof(from_c = false)

Enable the debugger:

ENV["JULIA_DEBUG"] = MatchSequences