Fixes for missense badness training/validation/testing

[lw453]

PR contains the following minor changes:

• Bug fixes in resource paths and variable placement introduced in https://github.com/broadinstitute/regional_missense_constraint/pull/285
• Fix for description of adj_freq_index parameter in some functions that were missed in https://github.com/broadinstitute/regional_missense_constraint/pull/286
• Addition of temporary storage of an aggregator that is created in prepare_amino_acid_ht of missense badness model generation which was slowing down runtime quite a bit
• Addition of code to save observed and possible counts in misbad HT (for use in misbad exploratory analyses)
• Update to logged information

[lw453]

Also added fixes to documentation typos introduced in https://github.com/broadinstitute/regional_missense_constraint/pull/284 and simplified transcript filtering method in prepare_amino_acid_ht.