bamCompare --scaleFactor console info

[dpryan79]

I presume that "Normalization: depth" is still printed to the screen if one manually sets a --scaleFactor. A better method would be to just print whatever was specified by the user.

[vivekbhr]

As far as I saw, the scale factors would be multiplied by the kept_reads/total_reads, which in absence of blacklist would be 1, so normalization: depth is not correct there as well..

[dpryan79]

I think in bamCompare the scale factors override the depth normalization rather than getting multiplied by it (I'm double checking this now). But if not I totally agree that this needs to be fixed too.

[dpryan79]

Actually, it seems that "Normalization: depth" will only be printed with bamCoverage. I'm not sure if the person who mentioned this on the mailing list mistook bamCoverage for bamCompare or not.

[dpryan79]

Gah, it's me who misread!

[dpryan79]

Hmm, it looks like "Normalization: none (signal scaled by percent alignment kept after filtering)" would be more appropriate. I added the current print out in #366, so I guess I can take the initiative to change it.

[dpryan79]

@vivekbhr What's your opinion of the changed wording in this commit?

[vivekbhr]

Sounds ok to me.. Can also write : signal scaled by the fraction of alignments kept after filtering

[dpryan79]

@vivekbhr Sounds good, changed and merged :)