genometools/genometools — pull request #329 by satta (2014-06-08 14:57:58+00:00)
Title: Improvement of speck tool

This PR adds the following improvements in the `gt speck` tool:
- Lua spec file namespace now provides a *GtFeatureIndex* of all features in input annotation if option `-provideindex` is given (in global variable `feature_index`)
- Lua spec file namespace now provides a *GtRegionMapping* for external sequence access if `-seqfile(s)`, `-encseq` or `-regionmapping` is given. Also requires one of `-matchdesc` etc.
- Added option `-sort` to sort input if desired
- Added the usual output file options (`-o`, `-force`, compression etc.). Useful for later output in other formats (JSON/...)
- Activate tidy mode for input by default and collect parser warnings into the rest of the checker output
- By default the tool now outputs statistics on a per-node basis (more intuitive to understand). Raw per-expectation stats are available with `-allexpects`.