[2/4] Add a --drop-n / -N option to drop any sequence containing an N #35
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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).
This is a stricter version of --truncate-n which may use sequence fragments up until the first N provided they pass the length filter.
Author
tsibley
changed the title
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This is a stricter version of --truncate-n which may use sequence
fragments up until the first N provided they pass the length filter.
Note: this depends on my previous branch (PR #34) and so contains those commits as well. Only the tip commit is the feature-adding one.