Adding freeze argument and allowing for easier re-runs

[ch-kr]

Major changes:

• Re-added save chi square HT option for single break search to allow for easier re-runs (avoid needing to re-run round 1 of single break search)
• Added freeze argument to pipeline and utility scripts missed last round

Minor changes:

• Added option to initialize Hail quietly (I want to test how how this looks)

[ch-kr]

Additional changes:

• Fixed build_models calls (removed trimers arg)
• Updated from using truncated chi square value to full value (using hl.qchisqtail)
• Added P_VALUE constant
• Added new MIN_EXP_MIS constant and set it to 16.0
• Added MIN_CHISQ_THRESHOLD constant
• Changed Batch billing project from gnomad-production > rmc-production
• Fixed additional pylint errors (CURRENT_FREEZE imports)

[lw453]

Additional comments:

• Reference to grouped_single_no_break_ht_path in prepare_transcripts.py doesn't have a freeze argument passed in - should we add this?
• We can change line 231 in rmc.py in single_search_round_ht_path() to return f"{single_search_bucket_path(search_num, freeze)}/{break_status}{breakpoint_status}.ht"
• I think we should add the freeze argument to merge_rmc_hts and consequently merge_round_no_break_ht since it uses single_search_round_ht_path and simul_search_round_bucket_path (currently with the default CURRENT_FREEZE)

Places where we need to add freeze to a temp filename:

• Line 333 in regional_constraint.py: f"{TEMP_PATH_WITH_FAST_DEL}/round{args.search_num}_temp.ht",
• Line 547 in regional_constraint.py: f"{TEMP_PATH_WITH_SLOW_DEL}/rmc_results.ht",
• Line 522 in constraint.py: f"{TEMP_PATH_WITH_FAST_DEL}/group_max_chisq.ht", overwrite=True
• Line 641 in constraint.py: f"{temp_path}/round{search_num}_all_loci_chisq.ht", overwrite=True (if saved in TEMP_PATH_WITH_FAST_DEL
• Line 1095 in constraint.py: f"{TEMP_PATH_WITH_FAST_DEL}/search_union.ht", overwrite=True

[ch-kr]

addressed comments above and also added:

• Command line arg to toggle whether to save all loci chi square HT for single and simul break searches
• Add structure to the merged no break/break HTs (so they don't write to top level RMC temp bucket)