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The path:

/home/xiaojing/codes/methpipe/src/smithlab_cpp/

has been hardcoded in the base-level Makefile, so it is impossible for this to compile for anyone other than Liz.

At least one file has an outdated copyright notice without the proper people or year.

Those are not standard, and cause compiler warnings. An example is "tolerance" in distribution.hpp, line 38.

It looks like someone has an editor that has unusual tab stops, or maybe is not properly converting tabs into spaces. Smith lab convention is that all tabs should be auto-converted to spaces, and every tab-stop should correspond to 2 spaces.

make: *** No rule to make target /home/xiaojing/codes/methpipe/src/smithlab_cpp/GenomicRegion.o', needed byinverted-dups'. Stop.

This is not a good thing to do. The word "new" has meaning in C++, so it's best to avoid it, for example in some name like "my_new_variable".

Something I asked about multiple times. Is it true that the T/C wildcards should be happening at the same time as the A/G wildcards? In other words, should the function:

static bool
similar_letters_bisulfite(const char a, const char b) {
return (a == b) || (a == 'T' && b == 'C') || (a == 'G' && b == 'A');
}

actually be two functions:

static bool
similar_letters_bisulfite_CT(const char a, const char b) {
return (a == b) || (a == 'T' && b == 'C');
}

static bool
similar_letters_bisulfite_GA(const char a, const char b) {
return (a == b) || (a == 'G' && b == 'A');
}

This repo contains executable binaries.

An old .svn directory somehow is appearing in the repo.

Files have been added to the repo with the only comment being "first version" which makes it pretty hard to figure out which file has what purpose. This should be fixed if possible by adding a comment retroactively.

This problem must stop happening.

Lines should almost never go beyond 80 characters.

These need to be removed.

This was obviously copied from somewhere, and no attention was paid to making sure it makes sense.

Not included by copying into the repo.

One example is inverted-dups