Added thresholding paths by count; Added Circos plot generation

Highlights:
1. path thresholding
2. circos plot generation
3. Coverity Scan, HipChat notifications and mac os x travis builds
4. ctx_thread.c handles cmdline arguments with getopts - begin phasing out cmd.c

== Cleaning Paths ==

ctx_thread.c:
- rewrite to load only accept one graph colour on the command line
- handle command line options itself, instead of using CmdArgs

generate_paths.c:
- update more stats about seqeunce coverage

graph_paths.c:
- sets path count in byte after path sequence in PathStore
- removes paths below a given threshold when doing removing of redundant paths
- updates PathStore given an updated PathSet

path_store.c:
- fixed bug in _path_store_add_to_hash() where PathHash pindex was not being set
  when loading from path file (.ctp).
- when loading ctp file for read threading, set loaded paths to count 255
- added path_store_counts_histogram() to get histogram of path counts -
  not used yet, should use in calculating threshold.

path_set.c:
- fixed BUG in path_set_slim() where excess paths may be kept
- added path_set_load_counts() to load PathSet counts from PathStore
- added path_set_threshold() to reduce a PathSet to only trustable paths
- added path_set_check() to check pointers are valid

== Other ==

path_hash.h:
- added PHASH_ITERATE() MACRO to iterate over paths

ctx_rmsubstr.c:
- support for reads that start with Ns
- report number of 'bad' reads which lack a kmer of {ACGT} bases
- added additional tests

ctx_join.c:
- add free() calls that were missing on exit

ctx_pjoin.c:
- add -t <threads> option

ctx_place.c:
- got rid of chrom_t type, used seq_load_all_reads() common function instead

breakpoint_caller.c:
- print reference contig names and lengths in header

.travis.yml:
- added coverity-scan* intergration
- added osx and linux compilation
- added hipchat notifications

./scripts/make-circos.pl:
- added perl script to generate a circos plot from breakpoint calls

* Coverity Scan was very useful in catching some bugs that are fixed in
  this commit. Their free service for Open Source projects is very cool.