ctx_rmsubstr.c:
- new command to remove substrings and duplicate strings from a set of strings

file_util.c:
- added futil_open_output(), futil_gzopen_output() for convenience. Open stdout
  if path is "-". Print status updates and die with appropriate message on error

seq_reader.c:
- added seq_load_all_reads() to load all reads in multiple files into a buffer

ctx_breakpoints.c:
- improve memory calculation by including graph annotation memory with graph mem
- reduce amount of memory required for bucket locks (we were wasteful before)
- truncate and remove commas and colons from chromosome names

ctx_subgraph.c, ctx_coverage.c:
- update usage message to match current behaviour

kmer_occur.c:
- we do not need to require db_graph->col_edges be allocated
- added check for allocation of bktlocks (for multithreaded graph modification)
- added check that we do not have more than 1 edge colour