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update gfaffix to v0.2.0 #1580

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merged 4 commits into from
Jan 13, 2025
+9 −12
Merged

update gfaffix to v0.2.0 #1580

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7d2b67d
update gfaffix to v0.2.0
glennhickey Jan 5, 2025
fa7be26
set gfaffix cores
glennhickey Jan 5, 2025
55efa9d
no longer use -W option when converting graphs for GFAffix since it s…
Jan 6, 2025
1a5d116
Merge branch 'danydoerr-master' into docker-fixes
glennhickey Jan 13, 2025
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10 changes: 5 additions & 5 deletions build-tools/downloadPangenomeTools
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Original file line number Diff line number Diff line change
Expand Up @@ -309,12 +309,12 @@ fi

# gfaffix
cd ${pangenomeBuildDir}
wget -q https://github.com/marschall-lab/GFAffix/releases/download/0.1.5b/GFAffix-0.1.5b_linux_x86_64.tar.gz
tar xzf GFAffix-0.1.5b_linux_x86_64.tar.gz
chmod +x GFAffix-0.1.5b_linux_x86_64/gfaffix
if [[ $STATIC_CHECK -ne 1 || $(ldd GFAffix-0.1.5b_linux_x86_64/gfaffix | grep so | wc -l) -eq 0 ]]
wget -q https://github.com/marschall-lab/GFAffix/releases/download/0.2.0/GFAffix-0.2.0_linux_x86_64.tar.gz
tar xzf GFAffix-0.2.0_linux_x86_64.tar.gz
chmod +x GFAffix-0.2.0_linux_x86_64/gfaffix
if [[ $STATIC_CHECK -ne 1 || $(ldd GFAffix-0.2.0_linux_x86_64/gfaffix | grep so | wc -l) -eq 0 ]]
then
mv GFAffix-0.1.5b_linux_x86_64/gfaffix ${binDir}
mv GFAffix-0.2.0_linux_x86_64/gfaffix ${binDir}
else
exit 1
fi
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11 changes: 4 additions & 7 deletions src/cactus/refmap/cactus_graphmap_join.py
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Expand Up @@ -685,20 +685,17 @@ def clip_vg(job, options, config, vg_path, vg_id, phase):
normalized_path = vg_path + '.gfaffixed'
gfa_in_path = vg_path + '.gfa'
gfa_out_path = normalized_path + '.gfa'
# GFAffix's --dont_collapse option doesn't work on W-lines, so we strip them for now with -W
cactus_call(parameters=['vg', 'convert', '-W', '-f', vg_path], outfile=gfa_in_path, job_memory=job.memory)
fix_cmd = ['gfaffix', gfa_in_path, '--output_refined', gfa_out_path, '--check_transformation']
# GFAffix supports W-lines as reference paths since v0.2.0
cactus_call(parameters=['vg', 'convert', '-f', vg_path], outfile=gfa_in_path, job_memory=job.memory)
fix_cmd = ['gfaffix', gfa_in_path, '--output_refined', gfa_out_path, '--check_transformation', '--threads', str(job.cores)]
if options.reference:
fix_cmd += ['--dont_collapse', options.reference[0] + '#[.]*']
cactus_call(parameters=fix_cmd, job_memory=job.memory)
# GFAffix strips the header, until this is fixed we need to add it back (for the RS tag)
gfa_header = cactus_call(parameters=['head', '-1', gfa_in_path], check_output=True).strip()
cactus_call(parameters=['sed', '-i', gfa_out_path, '-e', '1s/.*/{}/'.format(gfa_header)])
# Come back from gfa to vg
conv_cmd = [['vg', 'convert', '-g', '-p', gfa_out_path]]
# GFAFfix doesn't unchop, so we do that in vg after
conv_cmd.append(['vg', 'mod', '-u', '-'])
cactus_call(parameters=conv_cmd, outfile=normalized_path)
cactus_call(parameters=conv_cmd, outfile=normalized_path)
vg_path = normalized_path

# run clip-vg no matter what, but we don't actually remove anything in full
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