shendurelab / LACHESIS

The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)
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small changes to stop annoying segfaults #17

Closed abelew closed 7 years ago

abelew commented 7 years ago

Hi, Someone at school wants to use lachesis, but found it segmentation faulting. With a little fiddling, I found a few likely candidates (Time() attempting to write to read-only strings) and removed them. I also did a small amount of tidying with suggestions from clang-tidy and removed all references to ~/public_html/. Finally, I changed all the shebang entries to #!/usr/bin/env perl|Rscript rather than the hard-coded paths.

With these changes I am able to successfully run with the test data on our cluster (gcc 4.8, boost 1.61).

With your permission, I would like to invoke clang-tidy on the rest of the code and perform somewhat more invasive cleanups as well as make the output paths in .R and .pl configurable rather than the currently hard-coded values.