ekg/mutatrix

genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms

mutatrix's Issues

fastahack compile error on MAC OS

Hi,

when compiling on MAC OS using Homebrew g++ 4.9.3 I run into the following error:

cd fastahack && /Applications/Xcode.app/Contents/Developer/usr/bin/make
g++ -c Fasta.cpp
In file included from Fasta.h:19:0,
                 from Fasta.cpp:9:
LargeFileSupport.h:12:9: error: '__off64_t' does not name a type
 typedef __off64_t off_type;
         ^

I tried replacing the fastahack folder by the version of vg, but then I run into another issue:

g++ mutatrix.cpp \
		fastahack/Fasta.o -o mutatrix -Ivcflib/src/ -Ivcflib/ -L. -Lvcflib/tabixpp/ -ltabix -Lvcflib/ -lvcflib -lm -lz -std=c++0x
Undefined symbols for architecture x86_64:
  "repeatCounts(long, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)", referenced from:
      _main in ccBqFQjn.o

Any help would be appreciated.

Error compiling with gcc-10.1.0

Hi Erik,

In order to compile mutatrix, I had to change two lines in vcflib/fsom/fsom.c to avoid a compiler error. The change made is following:

OLD: dist_i = abs(x - i) ;
NEW: dist_i = abs( static_cast<int>(x - i) );

Why an error occurred and change was needed is explained here: https://stackoverflow.com/a/50301673

Installation

I git cloned under the folder and "make" to complie, but failed. How can I install this?

cd vcflib && make libvcflib.a
make[1]: Entering directory /home/sp/Tools/mutatrix/vcflib' make[1]: *** No rule to make targetlibvcflib.a'. Stop.
make[1]: Leaving directory `/home/sp/Tools/mutatrix/vcflib'
make: *** [vcflib/libvcflib.a] Error 2