Runtime fixes for v4

[ch-kr]

PR contains changes needed to get RMC search pipeline to run on v4/GRCh38.

Major changes:

• Added support to filter on AN instead of coverage/adjust expected values using AN instead of coverage; rmc/utils/generic.py and rmc/utils/constraint.py
• Updated context HT processing within get_aa_from_context to keep all of the annotations to actually extra AA information; rmc/utils/generic.py
• Updated handling of transcripts with 0 expected values; rmc/utils/constraint.py
• Fixed browser HT reformatting to actually adjust start/stop coordinates; rmc/utils/constraint.py
• Updated globals annotation for browser RMC HT; rmc/utils/constraint.py -- NOTE that this code hasn't been tested (updated after I finished running)

Minor changes:

• Added naive_coalesce for RMC results HT; rmc/pipeline/regional_constraint.py
• Added arguments to toggle filtering to canonical and outlier transcripts;rmc/pipeline/regional_constraint.py, rmc/utils/constraint.py
• Added arguments to pipeline script to create transcript resources and separate context_with_oe creation from RMC results finalizing; rmc/pipeline/regional_constraint.py
• Added check for whether single breaks HT had 0 rows; rmc/pipeline/regional_constraint.py
• Fixed transcript_ref and transcript_cds creation (previous code was buggy); rmc/utils/data_loading.py
• Updated default version for transcript resources; rmc/resources/reference_data.py
• Added option to run all sections through simul search a single run through dataproc; rmc/pipeline/two_breaks/run_batches_dataproc.py
• Removed success TSV writes (no longer used/taking up unnecessary space); rmc/pipeline/two_breaks/run_batches.py
• Update output paths to point to TEMP_PATH_WITH_FAST_DEL for temporary files generated that aren't needed; rmc/utils/simultaneous_breaks.py
• naive_coalesce > repartition to avoid zip length mismatch error; rmc/utils/simultaneous_breaks.py
• Preemptively removed coverage filter in rmc/utils/mpc.py due to removal of coverage filtering criteria from keep_criteria
• Preemptively updated coverage filter in rmc/utils/missense_badness.py
• Updated constraint_flagfield name to constraint_flags and additional filter to ENST transcripts only; rmc/utils/generic.py

[ch-kr]

adding a comment that I used freeze 1 for preliminary results; we can either plan to keep this data freeze (which means we'd have to update FREEZES and CURRENT_FREEZE in rmc.py) or we can overwrite the results from this freeze when we are ready to rerun

[ch-kr]

also just updated call to annotate_exploded_vep_for_constraint_groupings in constraint.py to include coverage_expr arg due to PR that just got merged in gnomad_methods -- function now has/expects this arg