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Many options which required an argument were declared as taking an optional argument. The option handling loop, however, did not expect optional arguments. For example, passing "--qual-threshold 30" rather than "--qual-threshold=30" or "-q 30" led to a segfault when atoi() was passed NULL (optarg). There were other affected options as well. This commit correctly declares the required/optional/none status of option arguments and matches that short-form option spec. Presumably this was confusion between the entire option being optional and the option's argument being optional. The required option checking is done outside of getopt.
This will help keep them in sync when updating options.
The usage docs now indicate option arguments and are easier to read. If the usage was specifically requested with --help, then it is printed to stdout instead of stderr. This is useful for the common idiom of asking for help and piping to a pager like less or more (without redirecting stderr).
Silences warnings about //-style comments and long strings. Since kseq.h uses inline functions, a feature of C99, it's not useful pretending to be C89 compat (GCC's default).
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See commit messages for description.