No effect of --centerReads in bamCoverage

[fgeier]

Hi!
I was trying to center PE reads to fragment midpoints, taking only the 5' end of the first read pair into account, i.e., counting only the fragment midpoint in the coverage profile . However in all cases I tried with bamCoverage there was no effect of the --centerReads option. Am I missing something?
test.zip

[dpryan79]

Which version are you using?

[fgeier]

Sorry, I forgot to say: 3.0.0

[dpryan79]

Indeed, at the moment --centerReads and --Offset are mutually exclusive, with --Offset taking precedence. I guess the desired result would be to center and then take the offset of that, so I'll see if I can get that implemented for the 3.1.0 release.

[dpryan79]

This will now be supported in version 3.1.0 (due out in June).

[dpryan79]

BTW, --centerReads only really makes sense if --extendReads is used.