Enable CRH to filter out hmmsearch output hits covering little of the HMM

[tonyelewis]

Jon requests a CRH feature to filter out hmmsearch output hits covering little of the HMM

This would just apply to input from hmmsearch output files.

It would compare 100.0 * ( hmm_to +1 - hmm_from ) / hmm_length to some threshold (where hmm_length comes from the [M=296] part of the file) and filter out hits that failed the threshold.

Jon has given me an example data file (hslu.hmmsearch) and ID (dc_4dc3ac2c5e4a70703d5d9cf0ba2f0ac9) that I can try to use to build the feature and that I can then add as a test case.

[tonyelewis]

Jon and I have discussed a bit further about this. We propose:

• The option should have an implicit value of 80% (but Jon's checking this and will let me know if I should change it).
• It might be good if --apply-cath-rules implicitly turned this on at some pre-specified threshold for IDs that match /^dc_\w{32}$/.

[tonyelewis]

This has been done in 62fc29fc1fad5344f3365a40472bcb88aead8be2 (with extra tests added in d92ad056734d3ffbbc68b9b81ccf0611dd87bdd7).

Thanks to 93c9b8e31143e57a5d4ded75b3ea7d02c85a3134, the hidden options can now be seen using the (hidden) options --hidden-help.