KNETFILE_HOOKS for using alternate network library

[AngieHinrichs]

The UCSC Genome Browser code base includes a network library with an interface analogous to knetfile.c's, but with a few extra features (HTTPS, u/p authentication, sparse file caching of complete URL paths). In order to use UCSC's network library within samtools, I have added a layer of indirection to knetfile functions. An alternate implementation of knetfile functions can be registered by passing in function pointers. Then, when a knetfile function is called, if an alternate function pointer has been registered, the knetfile function calls the alternate function and returns. The new code is all inside "#ifdef KNETFILE_HOOKS" so if -DKNETFILE_HOOKS is omitted, then samtools is compiled without the new layer.

The slight change to knetfile_hooks required a little extra abstraction in a couple other places in the code; for example, in bam_index_load_core, #ifdef KNETFILE_HOOKS then instead of saving the index file to the local directory and accessing it with fread, the index file is accessed using knetfile.

This patch also #ifdef 0's out the EOF check in bam.c, because I considered it costly & unnecessary for the Genome Browser's purposes -- I'd understand if you want to exclude that part. A separate #ifdef for it would be nice, though.

This patch has been in use for over a year in the UCSC Genome Browser and several of our mirror sites. I have provided versions of the patch with different line numbers for different samtools releases, along with instructions for applying the patch, here: http://genomewiki.ucsc.edu/index.php/KNETFILE_HOOKS . Some mirror maintainers have asked that I submit this, in hopes they won't have to manually patch every time they get the latest version of samtools.

I hope you'll consider incorporating this into samtools. Thanks!