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remove -V since I'm trying to get rid of the option #865

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remove -V since I'm trying to get rid of the option #865

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b18709c
remove -V since I'm trying to get rid fo the option
faithokamoto Mar 17, 2026
a4f4e12
more removal
faithokamoto Mar 17, 2026
6fffa11
add this back
faithokamoto Mar 18, 2026
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16 changes: 4 additions & 12 deletions src/toil_vg/vg_construct.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1568,28 +1568,20 @@ def run_make_haplo_thread_graphs(job, context, vg_id, vg_name, output_name, chro
cmd = ['vg', 'paths', '-d', '-v', os.path.basename(vg_path)]
with open(os.path.join(work_dir, base_graph_filename), 'wb') as out_file:
context.runner.call(job, cmd, work_dir = work_dir, outfile = out_file)
path_graph_filename = '{}{}_thread_{}_path.vg'.format(output_name, tag, hap)

vg_with_thread_as_path_path = os.path.join(work_dir, '{}{}_thread_{}_merge.vg'.format(output_name, tag, hap))

# get haplotype thread paths from the gbwt
cmd = ['vg', 'paths', '--gbwt', os.path.basename(gbwt_path), '--extract-vg', '-x', os.path.basename(xg_path)]
cmd = ['vg', 'paths', '--gbwt', os.path.basename(gbwt_path), '--retain-paths', '-x', os.path.basename(xg_path)]
for chrom in chroms:
# TODO: vg as of 1.39 can currently only support one
# selection at a time, and will fail if more are provided.
cmd += get_haplotype_selection_options(sample, chrom, hap)
with open(os.path.join(work_dir, path_graph_filename), 'wb') as out_file:
context.runner.call(job, cmd, work_dir = work_dir, outfile = out_file)

# Now combine the two files, adding the paths to the graph
vg_with_thread_as_path_path = os.path.join(work_dir, '{}{}_thread_{}_merge.vg'.format(output_name, tag, hap))
logger.info('Creating thread graph {}'.format(vg_with_thread_as_path_path))
cmd = ['vg', 'combine', '-c', base_graph_filename, path_graph_filename]
with open(vg_with_thread_as_path_path, 'wb') as out_file:
context.runner.call(job, cmd, work_dir = work_dir, outfile = out_file)

# Now delete the intermediates
os.unlink(os.path.join(work_dir, base_graph_filename))
os.unlink(os.path.join(work_dir, path_graph_filename))

# Now trim the graph vg_with_thread_as_path_path into vg_trimmed_path, dropping anything not covered by a path
vg_trimmed_path = os.path.join(work_dir, '{}{}_thread_{}.vg'.format(output_name, tag, hap))
Expand Down Expand Up @@ -1747,7 +1739,7 @@ def run_make_sample_region_graph(job, context, vg_id, vg_name, output_name, chro
with open(paths_path, 'wb') as paths_file:
# If we have a nonzero thread count we must have a GBWT.
# Get haplotype thread paths from the index for all haplotypes of the sample.
cmd = ['vg', 'paths', '--gbwt', os.path.basename(gbwt_path), '--extract-vg']
cmd = ['vg', 'paths', '--gbwt', os.path.basename(gbwt_path), '--retain-paths']
cmd += ['-x', os.path.basename(xg_path)]
cmd += get_haplotype_selection_options(sample)
context.runner.call(job, cmd, work_dir = work_dir, outfile = paths_file)
Expand Down