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Remove counter in normalised deltachi2 + fix iteration number in alignlog.

Biljana Mitreska requested to merge bimitres-normdeltachi2 into master
  • Normalised deltachi2 is a parameter that we want to monitor per iteration and is not supposed to be summed as it should get smaller with iteration. The counter was introduced in !195 (merged), this merge request reverts this back.
  • When alignment is run with iteration number is not written correctly in alignlog.txt (always stays at zero) because always runs one iteration. This merge request contains workaround so that the iteration number is saved properly in the alignlog. We need this to be fixed as in monitoring we are using this number.

@freiss @sborghi

Edited by Biljana Mitreska

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