[Bioperl-l] Update of bioperl-ext for modern environment

[Thomas Jahns]

Hello everyone,

I hope I  didn't duplicate anyone's work, but I couldn't find anything on this in the archives and so I patched bioperl-ext-1.5.1 to work with

- bioperl-1.5.2_102
- staden io_lib 1.11.4

and not crash perl.

Please see attached patch, I hope someone reading here can integrate it with the repository.

There is one necessary externally visible change: instead of specifiyng /foo/include/io_lib for the headers of the staden package, one now needs to specify /foo/include, because read.h includes other files with io_lib prefix.

I hope I removed the double-free bug in the right place, if the free'ing of a pointer passed into the function pgreen was intentional, another strategy will be needed.

Also I found make clean to be dysfunctional, but I don't know enough about MakeMaker to fix that, thus for recompiles I used a script for cleanup (also attached).


Greetings,
Thomas Jahns
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