D-Genies
v1.3.0
Python packages & modules
Javascript client functions
D-Genies
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Index
Symbols
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A
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B
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C
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D
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E
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F
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G
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
Symbols
$.fn.mousetip() ($.fn method)
A
allowed_file() (dgenies.lib.functions.Functions static method)
ask_for_upload() (dgenies.database.Session method)
ask_upload() (in module dgenies.views)
B
BaseModel (class in dgenies.database)
batch_type (dgenies.database.Job attribute)
bin
module
build_fasta() (in module dgenies.views)
build_list_no_assoc() (dgenies.lib.paf.Paf method)
build_query_as_reference() (in module dgenies.views)
build_query_chr_as_reference() (dgenies.lib.paf.Paf method)
build_query_on_target_association_file() (dgenies.lib.paf.Paf method)
build_summary_stats() (dgenies.lib.paf.Paf method)
C
check_file() (dgenies.lib.job_manager.JobManager method)
check_job_status_sge() (dgenies.lib.job_manager.JobManager method)
check_job_status_slurm() (dgenies.lib.job_manager.JobManager method)
check_job_success() (dgenies.lib.job_manager.JobManager method)
cleaner() (in module dgenies.bin.local_scheduler)
clear() (dgenies.lib.crons.Crons method)
(dgenies.lib.job_manager.JobManager method)
compress() (dgenies.lib.functions.Functions static method)
compress_and_send_mail() (dgenies.lib.functions.Functions static method)
compute_gravity_contigs() (dgenies.lib.paf.Paf method)
config (dgenies.lib.functions.Functions attribute)
(dgenies.lib.paf.Paf attribute)
connect() (dgenies.database.BaseModel class method)
contact() (in module dgenies.views)
Crons (class in dgenies.lib.crons)
D
d3.boxplot.__draw_idy_lines() (d3.boxplot method)
d3.boxplot.__lineFunction() (d3.boxplot method)
d3.boxplot._get_line_len() (d3.boxplot method)
d3.boxplot._sort_color_idy() (d3.boxplot method)
d3.boxplot._sort_lines() (d3.boxplot method)
d3.boxplot._sort_lines_by_idy() (d3.boxplot method)
d3.boxplot.change_color_theme() (d3.boxplot method)
d3.boxplot.draw() (d3.boxplot method)
d3.boxplot.draw_axis_bckgd() (d3.boxplot method)
d3.boxplot.draw_bottom_axis() (d3.boxplot method)
d3.boxplot.draw_left_axis() (d3.boxplot method)
d3.boxplot.draw_legend() (d3.boxplot method)
d3.boxplot.draw_lines() (d3.boxplot method)
d3.boxplot.draw_right_axis() (d3.boxplot method)
d3.boxplot.draw_top_axis() (d3.boxplot method)
d3.boxplot.events.filter_identity() (d3.boxplot.events method)
d3.boxplot.events.filter_size() (d3.boxplot.events method)
d3.boxplot.events.init() (d3.boxplot.events method)
d3.boxplot.events.init_context_menu() (d3.boxplot.events method)
d3.boxplot.events.set_break_lines_visibility() (d3.boxplot.events method)
d3.boxplot.events.stroke_linecap() (d3.boxplot.events method)
d3.boxplot.events.stroke_width() (d3.boxplot.events method)
d3.boxplot.get_human_readable_size() (d3.boxplot method)
d3.boxplot.init() (d3.boxplot method)
d3.boxplot.launch() (d3.boxplot method)
d3.boxplot.mousetip.get_label() (d3.boxplot.mousetip method)
d3.boxplot.mousetip.get_match() (d3.boxplot.mousetip method)
d3.boxplot.mousetip.getColorByBgColor() (d3.boxplot.mousetip method)
d3.boxplot.mousetip.hide() (d3.boxplot.mousetip method)
d3.boxplot.mousetip.init() (d3.boxplot.mousetip method)
d3.boxplot.select_query() (d3.boxplot method)
d3.boxplot.select_target() (d3.boxplot method)
d3.boxplot.select_zone() (d3.boxplot method)
d3.boxplot.switch_color_theme() (d3.boxplot method)
d3.boxplot.zoom._cursor_pos() (d3.boxplot.zoom method)
d3.boxplot.zoom.click() (d3.boxplot.zoom method)
d3.boxplot.zoom.init() (d3.boxplot.zoom method)
d3.boxplot.zoom.mousedown() (d3.boxplot.zoom method)
d3.boxplot.zoom.mouseup() (d3.boxplot.zoom method)
d3.boxplot.zoom.reset_scale() (d3.boxplot.zoom method)
d3.boxplot.zoom.restore_scale() (d3.boxplot.zoom method)
d3.boxplot.zoom.translate() (d3.boxplot.zoom method)
d3.boxplot.zoom.zoom() (d3.boxplot.zoom method)
d3.boxplot.zoom_bottom_axis() (d3.boxplot method)
d3.boxplot.zoom_left_axis() (d3.boxplot method)
Database (class in dgenies.database)
date_created (dgenies.database.Job attribute)
(dgenies.database.Session attribute)
delete() (dgenies.lib.job_manager.JobManager method)
delete_job() (in module dgenies.views)
dgenies
module
dgenies.ajax() (dgenies method)
dgenies.bin.clean_jobs
module
dgenies.bin.filter_contigs
module
dgenies.bin.index
module
dgenies.bin.local_scheduler
module
dgenies.bin.merge_splitted_chrms
module
dgenies.bin.sort_paf
module
dgenies.bin.split_fa
module
dgenies.config_reader
module
dgenies.database
module
dgenies.documentation.fix_links_headers() (dgenies.documentation method)
dgenies.documentation.goto() (dgenies.documentation method)
dgenies.documentation.init() (dgenies.documentation method)
dgenies.fill_select_zones() (dgenies method)
dgenies.get() (dgenies method)
dgenies.hide_loading() (dgenies method)
dgenies.init() (dgenies method)
dgenies.lib
module
dgenies.lib.crons
module
dgenies.lib.decorators
module
dgenies.lib.drmaasession
module
dgenies.lib.fasta
module
dgenies.lib.functions
module
dgenies.lib.job_manager
module
dgenies.lib.latest
module
dgenies.lib.mailer
module
dgenies.lib.paf
module
dgenies.lib.parsers
module
dgenies.lib.upload_file
module
dgenies.lib.validators
module
dgenies.notify() (dgenies method)
dgenies.numberWithCommas() (dgenies method)
dgenies.post() (dgenies method)
dgenies.reset_loading_message() (dgenies method)
dgenies.result.add_to_list() (dgenies.result method)
dgenies.result.controls.delete_job() (dgenies.result.controls method)
dgenies.result.controls.do_delete_job() (dgenies.result.controls method)
dgenies.result.controls.init() (dgenies.result.controls method)
dgenies.result.controls.launch_hide_noise() (dgenies.result.controls method)
dgenies.result.controls.launch_reverse_contig() (dgenies.result.controls method)
dgenies.result.controls.launch_sort_contigs() (dgenies.result.controls method)
dgenies.result.controls.select_zone() (dgenies.result.controls method)
dgenies.result.controls.summary() (dgenies.result.controls method)
dgenies.result.export.ask_export_fasta() (dgenies.result.export method)
dgenies.result.export.dl_fasta() (dgenies.result.export method)
dgenies.result.export.export() (dgenies.result.export method)
dgenies.result.export.export_association_table() (dgenies.result.export method)
dgenies.result.export.export_backup_file() (dgenies.result.export method)
dgenies.result.export.export_fasta() (dgenies.result.export method)
dgenies.result.export.export_no_association_file() (dgenies.result.export method)
dgenies.result.export.export_offline_viewer() (dgenies.result.export method)
dgenies.result.export.export_paf() (dgenies.result.export method)
dgenies.result.export.export_png() (dgenies.result.export method)
dgenies.result.export.export_query_as_reference_fasta_standalone() (dgenies.result.export method)
dgenies.result.export.export_query_as_reference_fasta_webserver() (dgenies.result.export method)
dgenies.result.export.export_svg() (dgenies.result.export method)
dgenies.result.export.get_svg() (dgenies.result.export method)
dgenies.result.export.save_file() (dgenies.result.export method)
dgenies.result.init() (dgenies.result method)
dgenies.result.remove_job_from_cookie() (dgenies.result method)
dgenies.result.summary._get_label() (dgenies.result.summary method)
dgenies.result.summary.export_png() (dgenies.result.summary method)
dgenies.result.summary.export_svg() (dgenies.result.summary method)
dgenies.result.summary.export_tsv() (dgenies.result.summary method)
dgenies.result.summary.get_svg() (dgenies.result.summary method)
dgenies.result.summary.save_file() (dgenies.result.summary method)
dgenies.result.summary.show() (dgenies.result.summary method)
dgenies.run.__upload_server_error() (dgenies.run method)
dgenies.run._init_fileupload() (dgenies.run method)
dgenies.run._set_file_event() (dgenies.run method)
dgenies.run._set_file_select_event() (dgenies.run method)
dgenies.run._start_upload() (dgenies.run method)
dgenies.run.add_error() (dgenies.run method)
dgenies.run.allowed_file() (dgenies.run method)
dgenies.run.ask_for_upload() (dgenies.run method)
dgenies.run.change_fasta_type() (dgenies.run method)
dgenies.run.check_url() (dgenies.run method)
dgenies.run.disable_form() (dgenies.run method)
dgenies.run.do_submit() (dgenies.run method)
dgenies.run.enable_form() (dgenies.run method)
dgenies.run.fill_examples() (dgenies.run method)
dgenies.run.get_file_size_str() (dgenies.run method)
dgenies.run.hide_loading() (dgenies.run method)
dgenies.run.hide_success() (dgenies.run method)
dgenies.run.init() (dgenies.run method)
dgenies.run.init_fileuploads() (dgenies.run method)
dgenies.run.ping_upload() (dgenies.run method)
dgenies.run.reset_errors() (dgenies.run method)
dgenies.run.reset_file_form() (dgenies.run method)
dgenies.run.reset_file_input() (dgenies.run method)
dgenies.run.restore_form() (dgenies.run method)
dgenies.run.set_events() (dgenies.run method)
dgenies.run.set_filename() (dgenies.run method)
dgenies.run.show_global_loading() (dgenies.run method)
dgenies.run.show_loading() (dgenies.run method)
dgenies.run.show_success() (dgenies.run method)
dgenies.run.show_tab() (dgenies.run method)
dgenies.run.start_uploads() (dgenies.run method)
dgenies.run.submit() (dgenies.run method)
dgenies.run.upload_next() (dgenies.run method)
dgenies.run.valid_form() (dgenies.run method)
dgenies.save_cookies() (dgenies method)
dgenies.set_loading_message() (dgenies method)
dgenies.show_loading() (dgenies method)
dgenies.status.autoreload() (dgenies.status method)
dgenies.status.init() (dgenies.status method)
dgenies.tools
module
dgenies.update_results() (dgenies method)
dgenies.views
module
dl_fasta() (in module dgenies.views)
do_align() (dgenies.lib.job_manager.JobManager method)
documentation_dotplot() (in module dgenies.views)
documentation_formats() (in module dgenies.views)
documentation_result() (in module dgenies.views)
documentation_run() (in module dgenies.views)
DoesNotExist (dgenies.database.BaseModel attribute)
(dgenies.database.Gallery attribute)
(dgenies.database.Job attribute)
(dgenies.database.Session attribute)
download_file() (in module dgenies.views)
download_files_with_pending() (dgenies.lib.job_manager.JobManager method)
download_paf() (in module dgenies.views)
E
email (dgenies.database.Job attribute)
error (dgenies.database.Job attribute)
execute_sql() (dgenies.database.RetryOperationalError method)
F
Fasta (class in dgenies.lib.fasta)
Filter (class in dgenies.bin.filter_contigs)
filter() (dgenies.bin.filter_contigs.Filter method)
find_error_in_log() (dgenies.lib.job_manager.JobManager static method)
flush_contig() (dgenies.bin.split_fa.Splitter method)
free_noise() (in module dgenies.views)
Functions (class in dgenies.lib.functions)
G
Gallery (class in dgenies.database)
gallery() (in module dgenies.views)
gallery_file() (in module dgenies.views)
gallery_set (dgenies.database.Job attribute)
get_backup_file() (in module dgenies.views)
get_d3js_data() (dgenies.lib.paf.Paf method)
get_fasta_file() (dgenies.lib.functions.Functions static method)
get_file() (dgenies.lib.upload_file.UploadFile method)
(in module dgenies.views)
get_file_size() (dgenies.lib.job_manager.JobManager method)
get_filter_out() (in module dgenies.views)
get_filter_out_query() (in module dgenies.views)
get_filter_out_target() (in module dgenies.views)
get_gallery_items() (dgenies.lib.functions.Functions static method)
get_graph() (in module dgenies.views)
get_list_all_jobs() (dgenies.lib.functions.Functions static method)
get_mail_content() (dgenies.lib.job_manager.JobManager method)
get_mail_content_html() (dgenies.lib.job_manager.JobManager method)
get_mail_for_job() (dgenies.lib.functions.Functions static method)
get_mail_subject() (dgenies.lib.job_manager.JobManager method)
get_name() (dgenies.lib.fasta.Fasta method)
get_path() (dgenies.lib.fasta.Fasta method)
get_pending_local_number() (dgenies.lib.job_manager.JobManager static method)
get_prep_scheduled_jobs() (in module dgenies.bin.local_scheduler)
get_preparing_jobs_cluster_nb() (in module dgenies.bin.local_scheduler)
get_preparing_jobs_nb() (in module dgenies.bin.local_scheduler)
get_queries_on_target_association() (dgenies.lib.paf.Paf method)
get_query_as_reference() (in module dgenies.views)
get_query_on_target_association() (dgenies.lib.paf.Paf method)
get_query_split() (dgenies.lib.job_manager.JobManager method)
get_readable_size() (dgenies.lib.functions.Functions static method)
get_readable_time() (dgenies.lib.functions.Functions static method)
get_scheduled_cluster_jobs() (in module dgenies.bin.local_scheduler)
get_scheduled_local_jobs() (in module dgenies.bin.local_scheduler)
get_status_standalone() (dgenies.lib.job_manager.JobManager method)
get_summary_stats() (dgenies.lib.paf.Paf method)
get_tools_options() (in module dgenies.views)
get_type() (dgenies.lib.fasta.Fasta method)
get_valid_uploaded_filename() (dgenies.lib.functions.Functions static method)
get_viewer_html() (in module dgenies.views)
getting_files() (dgenies.lib.job_manager.JobManager method)
global_templates_variables() (in module dgenies.views)
I
id (dgenies.database.BaseModel attribute)
(dgenies.database.Gallery attribute)
(dgenies.database.Job attribute)
(dgenies.database.Session attribute)
id_job (dgenies.database.Job attribute)
id_process (dgenies.database.Job attribute)
Index (class in dgenies.bin.index)
index_file() (in module dgenies.bin.index)
init_clean_cron() (dgenies.lib.crons.Crons method)
init_launch_local_cron() (dgenies.lib.crons.Crons method)
install() (in module dgenies.views)
is_contig_well_oriented() (dgenies.lib.paf.Paf method)
is_example() (dgenies.lib.fasta.Fasta method)
is_gz_file() (dgenies.lib.job_manager.JobManager static method)
is_in_gallery() (dgenies.lib.functions.Functions static method)
is_query_filtered() (dgenies.lib.job_manager.JobManager method)
is_target_filtered() (dgenies.lib.job_manager.JobManager method)
J
Job (class in dgenies.database)
job (dgenies.database.Gallery attribute)
job_id (dgenies.database.Gallery attribute)
JobManager (class in dgenies.lib.job_manager)
K
keep_active (dgenies.database.Session attribute)
keyerror_message() (dgenies.lib.paf.Paf method)
L
last_ping (dgenies.database.Session attribute)
Latest (class in dgenies.lib.latest)
launch() (dgenies.lib.job_manager.JobManager method)
(in module dgenies)
launch_analysis() (in module dgenies.views)
launch_standalone() (dgenies.lib.job_manager.JobManager method)
launch_to_cluster() (dgenies.lib.job_manager.JobManager method)
legal() (in module dgenies.views)
limit_idy (dgenies.lib.paf.Paf attribute)
load() (dgenies.bin.index.Index static method)
(dgenies.lib.latest.Latest method)
load_query_index() (dgenies.bin.merge_splitted_chrms.Merger method)
M
maf() (in module dgenies.lib.parsers)
(in module dgenies.lib.validators)
Mailer (class in dgenies.lib.mailer)
main() (in module dgenies.views)
mashmap2paf() (in module dgenies.lib.parsers)
max_nb_lines (dgenies.lib.paf.Paf attribute)
mem_peak (dgenies.database.Job attribute)
merge() (dgenies.bin.merge_splitted_chrms.Merger method)
merge_paf() (dgenies.bin.merge_splitted_chrms.Merger static method)
Merger (class in dgenies.bin.merge_splitted_chrms)
module
bin
dgenies
dgenies.bin.clean_jobs
dgenies.bin.filter_contigs
dgenies.bin.index
dgenies.bin.local_scheduler
dgenies.bin.merge_splitted_chrms
dgenies.bin.sort_paf
dgenies.bin.split_fa
dgenies.config_reader
dgenies.database
dgenies.lib
dgenies.lib.crons
dgenies.lib.decorators
dgenies.lib.drmaasession
dgenies.lib.fasta
dgenies.lib.functions
dgenies.lib.job_manager
dgenies.lib.latest
dgenies.lib.mailer
dgenies.lib.paf
dgenies.lib.parsers
dgenies.lib.upload_file
dgenies.lib.validators
dgenies.tools
dgenies.views
move_job_to_cluster() (in module dgenies.bin.local_scheduler)
MyRetryDB (class in dgenies.database)
N
name (dgenies.database.Gallery attribute)
nb_open (dgenies.database.Database attribute)
new() (dgenies.database.Session class method)
no_assoc() (in module dgenies.views)
O
options (dgenies.database.Job attribute)
P
Paf (class in dgenies.lib.paf)
paf() (in module dgenies.lib.validators)
parse_args() (in module dgenies.bin.local_scheduler)
(in module dgenies.bin.merge_splitted_chrms)
(in module dgenies.bin.split_fa)
parse_data_folders() (in module dgenies.bin.clean_jobs)
parse_database() (in module dgenies.bin.clean_jobs)
parse_index() (dgenies.lib.paf.Paf method)
parse_paf() (dgenies.lib.paf.Paf method)
parse_started_jobs() (in module dgenies.bin.local_scheduler)
parse_upload_folders() (in module dgenies.bin.clean_jobs)
parse_uploads_asks() (in module dgenies.bin.local_scheduler)
picture (dgenies.database.Gallery attribute)
ping() (dgenies.database.Session method)
ping_upload() (in module dgenies.views)
post_query_as_reference() (in module dgenies.views)
prepare_data() (dgenies.lib.job_manager.JobManager method)
prepare_data_cluster() (dgenies.lib.job_manager.JobManager method)
prepare_data_in_thread() (dgenies.lib.job_manager.JobManager method)
prepare_data_local() (dgenies.lib.job_manager.JobManager method)
prepare_dotplot_cluster() (dgenies.lib.job_manager.JobManager method)
prepare_dotplot_local() (dgenies.lib.job_manager.JobManager method)
prepare_job() (in module dgenies.bin.local_scheduler)
Q
qt_assoc() (in module dgenies.views)
query (dgenies.database.Gallery attribute)
query_fasta_file_exists() (dgenies.lib.functions.Functions static method)
R
random_string() (dgenies.lib.functions.Functions static method)
read_index() (dgenies.lib.functions.Functions static method)
remove_noise() (dgenies.lib.paf.Paf static method)
reorient_contigs_in_paf() (dgenies.lib.paf.Paf method)
result() (in module dgenies.views)
RetryOperationalError (class in dgenies.database)
reverse_contig() (dgenies.lib.paf.Paf method)
(in module dgenies.views)
run() (in module dgenies.views)
run_job() (dgenies.lib.job_manager.JobManager method)
run_job_in_thread() (dgenies.lib.job_manager.JobManager method)
run_test() (in module dgenies.views)
S
s_id (dgenies.database.Session attribute)
save() (dgenies.bin.index.Index static method)
save_json() (dgenies.lib.paf.Paf method)
search_error() (dgenies.lib.job_manager.JobManager method)
send_fasta_ready() (dgenies.lib.functions.Functions static method)
send_mail() (dgenies.lib.job_manager.JobManager method)
(dgenies.lib.mailer.Mailer method)
(in module dgenies.views)
send_mail_post() (dgenies.lib.job_manager.JobManager method)
Session (class in dgenies.database)
set_inputs_from_res_dir() (dgenies.lib.job_manager.JobManager method)
set_job_status() (dgenies.lib.job_manager.JobManager method)
set_name() (dgenies.lib.fasta.Fasta method)
set_path() (dgenies.lib.fasta.Fasta method)
set_sorted() (dgenies.lib.paf.Paf method)
set_status_standalone() (dgenies.lib.job_manager.JobManager method)
Singleton (class in dgenies.lib.decorators)
sort() (dgenies.bin.sort_paf.Sorter method)
(dgenies.lib.paf.Paf method)
sort_fasta() (dgenies.lib.functions.Functions static method)
sort_graph() (in module dgenies.views)
Sorter (class in dgenies.bin.sort_paf)
split() (dgenies.bin.split_fa.Splitter method)
split_contig() (dgenies.bin.split_fa.Splitter static method)
Splitter (class in dgenies.bin.split_fa)
start_all() (dgenies.lib.crons.Crons method)
start_job() (dgenies.lib.job_manager.JobManager method)
(in module dgenies.bin.local_scheduler)
status (dgenies.database.Job attribute)
(dgenies.database.Session attribute)
status() (dgenies.lib.job_manager.JobManager method)
(in module dgenies.views)
summary() (in module dgenies.views)
T
target (dgenies.database.Gallery attribute)
time_elapsed (dgenies.database.Job attribute)
Tool (class in dgenies.tools)
tool (dgenies.database.Job attribute)
U
uncompress() (dgenies.lib.functions.Functions static method)
unpack_backup() (dgenies.lib.job_manager.JobManager method)
update() (dgenies.lib.latest.Latest method)
update_async() (dgenies.lib.latest.Latest method)
update_job_status() (dgenies.lib.job_manager.JobManager method)
upload() (in module dgenies.views)
upload_folder (dgenies.database.Session attribute)
UploadFile (class in dgenies.lib.upload_file)
V
v_idx() (in module dgenies.lib.validators)
W
write_contig() (dgenies.bin.split_fa.Splitter static method)
write_query_index() (dgenies.bin.merge_splitted_chrms.Merger static method)
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