Optionally emit SV lengths

[yfarjoun]

closes #503

This PR adds a commandline argument that emits the lengths of the SVs found on the reads into the VCF record that contains the resulting SV. The argument is suppressed (not showing in the "help") and is prefixed with dev- to indicate that it's a development/debugging option.

The only change to the output is the (currently non-optional) addition of the SVLENGTHS header line in the VCF. However, I'm happy to make this also optional. otherwise, the algorithm and output are unchanged unless --dev-emit-sv-lengths is provided on the command-line.

[yfarjoun]

I'd love to know what needs to be done to get some traction on this PR. It doesn't change the default behaviour, but it allows users to better understand the distribution of svlengths that the call have and thus perform better clustering and other downstream analyses.

Please do consider these changes and let me know if there's anything I can do to make it easier for the maintainers.

[fritzsedlazeck]

Thanks @hermannromanek could you take a look?

[yfarjoun]

Hi, I know it's not easy to find time to maintain a OSS repo. If there's anything I can do to make it easier to review my PR, Please let me know!

[fritzsedlazeck]

Dear @yfarjoun Thanks. we are working on this. This is on me.. i wanted a development github that is private and this public facing github. so now Herman needs to merge before the new release and this is unfortunately the way these things are getting incorporated. Hope that kinda makes sense but we wanted to have a code environment that we can explore things with :). Thanks Fritz

[yfarjoun]

Thanks for the explanation @fritzsedlazeck, that makes total sense! I will not mis-take the silence for lack of response anymore 😄

[yfarjoun]

Thanks!! 🥳

[hermannromanek]

Preparing release 2.5 right now :)