[3/4] Optionally use a fixed window size instead of 0.1 of the read length #36
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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).
A fixed window size provides a stricter control on average base qualities for datasets with a wide range of read lengths.
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@xapple That's up to @najoshi, who seems to be pretty out of touch with the Github issues/PRs. You can always use the @MullinsLab sickle fork if you want, which does have this PR merged into it. |
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OK That's cool, maybe I'll try it out. But if you have forked and added features etc. you should definitely bump the version number and have sickle 1.34 |
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No, I'm not going to version our fork in the same space as @najoshi's. That would lead to much confusion. I did change how the version is displayed, however: MullinsLab@4b0dc85 |
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A fixed window size provides a stricter control on average base qualities for datasets with a wide range of read lengths.
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.