tools.js: get_mutations: deal with common gaps

As get_codons may return codons with gaps inside, testing for the codon length is not enough
we must first clean the codons by removing the common gaps.
However the codons must not be cleaned to early so that positions are properly counted.

See #2056
8 jobs for feature-c/2056-display-synonymous-mutations in 4 minutes and 41 seconds (queued for 5 seconds)
Status Job ID Name Coverage
  Test Tools
passed #172574
test_tools

00:00:09

failed #172567
test_tools

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  Test Quality
passed #172568
web
code_quality

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  Test Unit
passed #172569
web
test_browser_unit

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  Deploy Review
passed #172570
web
deploy_review

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manual #172571
web allowed to fail manual
stop_deploy_review
 
  Test Functional
passed #172572
web
test_browser-functional

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  Test Functional External
passed #172573
web
test_browser-functional-external

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