I undid the commits from Jan 13 because they were changes I did in September and rather more intrusive than I remembered.
The first commit adds in enough autotools logic to (at least on the 2 computers I tested) invoke ./configure ; make in order autodetect boost and build a static copy of lachesis which is sufficient for the folks here at umd to use it. I have only tested myself the test data, but have been told that it works for real data. Sadly, samtools is sufficiently non-standard that I got angry and just put its source tree into src/include/ -- which is unwise and should be undone once I figure out the proper autotools logic. This commit is slightly intrusive because it reorganizes the files in order to more closely follow the gnu conventions. I added the gnu convention files like Changelog, NEWS, etc; as well as a copy of the gnu modules file that I used to make lachesis available on our computing cluster.
The second commit results from me simple opening all the files in emacs and resaving them. I have a hook which calls delete-trailing-whitespace. It offends me, and when I go back to make actually substantive changes, I do not want hundreds of whitespace line changes confusing the issue.
Assuming this is acceptable, I am thinking to use the make tidy target I added to the Makefile in order to make some minor changes that should streamline the compile and potentially lower the stack space usage a bit, thus hopefully make it less likely to segfault.
I undid the commits from Jan 13 because they were changes I did in September and rather more intrusive than I remembered.
The first commit adds in enough autotools logic to (at least on the 2 computers I tested) invoke ./configure ; make in order autodetect boost and build a static copy of lachesis which is sufficient for the folks here at umd to use it. I have only tested myself the test data, but have been told that it works for real data. Sadly, samtools is sufficiently non-standard that I got angry and just put its source tree into src/include/ -- which is unwise and should be undone once I figure out the proper autotools logic. This commit is slightly intrusive because it reorganizes the files in order to more closely follow the gnu conventions. I added the gnu convention files like Changelog, NEWS, etc; as well as a copy of the gnu modules file that I used to make lachesis available on our computing cluster.
The second commit results from me simple opening all the files in emacs and resaving them. I have a hook which calls delete-trailing-whitespace. It offends me, and when I go back to make actually substantive changes, I do not want hundreds of whitespace line changes confusing the issue.
Assuming this is acceptable, I am thinking to use the make tidy target I added to the Makefile in order to make some minor changes that should streamline the compile and potentially lower the stack space usage a bit, thus hopefully make it less likely to segfault.