Edit help text to make clear when some codons are excluded by observedMutations

[Steven Kleinstein]

Edit help to make clear the behavior in the description below (from Jason)

...a mutation that introduces a stop codon, which observedMutations considers neither a replacement nor silent mutation. For example: SEQUNCE_IMGT> AAA GERMLINE_IMGT> TCA

The stop is introduced when the second A is considered as a mutation, because mutations are counted in the germline context individually. So TAA vs TCA and ACA vs TCA are both considered, with the TAA causing the exclusion of the codon.

Also, ... The codon would be excluded if the germline codon is ambiguous, .... For example: SEQUNCE_IMGT> TGG GERMLINE_IMGT> G.G So, long story short, there are few different cases where codons are excluded from the mutation counts due to stop codons or being unable to resolve replacement vs silent. Those cases are what's leading to the differences between nucleotide mismatches and mutation counts.

[Julian Zhou]

Commit 3d2ce16

• added an additional line of help to observedMutations, as Steven suggested (", including criteria for which sequence differences are included in the mutation counts and which are not.")

• expanded @details for calcObservedMutations, elaborating on what "independently in the germline context" means, as well as adding more examples for where certain mutations are excluded.