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disable outgroup computation for pangenomes #1441

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Merged
glennhickey merged 1 commit into from
Jul 18, 2024
Merged

disable outgroup computation for pangenomes #1441

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3 changes: 1 addition & 2 deletions src/cactus/refmap/cactus_graphmap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -114,8 +114,7 @@ def graph_map(options):
# load up the seqfile and figure out the outgroups and schedule
config_wrapper.substituteAllPredefinedConstantsWithLiterals(options)
mc_tree, input_seq_map, og_candidates = parse_seqfile(options.seqFile, config_wrapper, pangenome=True)
og_map = compute_outgroups(mc_tree, config_wrapper, set(og_candidates))
event_set = get_event_set(mc_tree, config_wrapper, og_map, mc_tree.getRootName())
event_set = get_event_set(mc_tree, config_wrapper, {}, mc_tree.getRootName())

# apply path overrides. this was necessary for wdl which doesn't take kindly to
# text files of local paths (ie seqfile). one way to fix would be to add support
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3 changes: 1 addition & 2 deletions src/cactus/refmap/cactus_refmap.py
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Expand Up @@ -297,8 +297,7 @@ def main():
config_wrapper = ConfigWrapper(config_node)
config_wrapper.substituteAllPredefinedConstantsWithLiterals(options)
mc_tree, input_seq_map, og_candidates = parse_seqfile(options.seqFile, config_wrapper)
og_map = compute_outgroups(mc_tree, config_wrapper, set(og_candidates))
event_set = get_event_set(mc_tree, config_wrapper, og_map, mc_tree.getRootName())
event_set = get_event_set(mc_tree, config_wrapper, {}, mc_tree.getRootName())

# apply path overrides. this was necessary for wdl which doesn't take kindly to
# text files of local paths (ie seqfile). one way to fix would be to add support
Expand Down
7 changes: 6 additions & 1 deletion src/cactus/setup/cactus_align.py
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Expand Up @@ -260,7 +260,12 @@ def make_align_job(options, toil, config_wrapper=None, chrom_name=None):

mc_tree, input_seq_map, og_candidates = parse_seqfile(options.seqFile, config_wrapper,
pangenome=options.pangenome)
og_map = compute_outgroups(mc_tree, config_wrapper, set(og_candidates), chrom_info_file = options.chromInfo)
if options.pangenome:
# outgroups not supported in pangenomes
# also, compute_outgroups() uses about 300 * N^2 bytes which can be huge for big pangenomes
og_map = {}
else:
og_map = compute_outgroups(mc_tree, config_wrapper, set(og_candidates), chrom_info_file = options.chromInfo)
event_set = get_event_set(mc_tree, config_wrapper, og_map, options.root if options.root else mc_tree.getRootName())
if options.includeRoot:
if options.root not in input_seq_map:
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