[1/4] Option sync and usage cleanup #40
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Standardizes on --truncate-n. This preserves the --trunc-n long name previously mentioned in the SE usage. It removes the --discard-n long name only ever used internally, but never documented.
This will help keep them in sync when updating options.
No functional change, only whitespace (compare with git diff -w).
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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This was referenced Feb 25, 2015
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@najoshi Thanks for recently fixing the option handling segfault that I had submitted PR #34 for a while back.
This is that PR rebased onto your current master since you duplicated the fix from the original first commit.
This PR:
--debugto both se and pe--truncate-n(instead of documenting--trunc-nin SE usage but only accepting--discard-n)Please let me know if you have any questions or concerns. I'm using a forked copy of sickle in various pipelines due to the changes I had to make, but I'd much rather get the fixes into your version of sickle so I can use the official one!