-n / -N options: Only consider Ns between the sliding window cut sites #39
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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).
A fixed window size provides a stricter control on average base qualities for datasets with a wide range of read lengths.
This is a stricter version of --truncate-n which may use sequence fragments up until the first N provided they pass the length filter.
Otherwise Ns that might otherwise be trimmed off will cause unnecessary read dropping. For example using --truncate-n, if an N occurs early in the sequence, it's possible for the 3' cut site to be set closer to the 5' end than the 5' cut site, which results in a dropped read due to negative length.
Perl's testing infrastructure is mature, well proven, and easy to extend. I've listed all the dependencies for completeness in test/cpanfile, used by `make install-test-deps`, but only one dep (Capture::Tiny) is not distributed with core Perl.
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Closing this PR in favor of #41, which is updated to be based upon your new work and mine. |
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Otherwise Ns that might otherwise be trimmed off will cause unnecessary
read dropping. For example using
--truncate-n, if an N occurs early inthe sequence, it's possible for the 3' cut site to be set closer to the
5' end than the 5' cut site, which results in a dropped read due to
negative length.
Note: this depends on my previous PRs #34, #35, and #36 and so contains those commits as well. Only the last two commits on the branch are the ones specific to this PR.