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rGFA support (experimental) #1186

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rGFA support (experimental) #1186

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61dbed5
add rgfa interface
glennhickey May 10, 2023
f34c56b
flesh out rgfa interface
glennhickey Oct 3, 2023
018f618
update to newer vg
glennhickey Oct 5, 2023
1c39998
update vg
glennhickey Oct 6, 2023
ae6985b
update vg again
glennhickey Oct 6, 2023
55e2770
0-haplotypes everywhere
glennhickey Oct 6, 2023
d30c5c2
Merge remote-tracking branch 'origin/master' into rgfa2
glennhickey Nov 21, 2023
1ba988f
fix rgfa/vcf option toggle--rgfa only works on backbone
glennhickey Nov 21, 2023
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3 changes: 2 additions & 1 deletion build-tools/downloadPangenomeTools
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Original file line number Diff line number Diff line change
Expand Up @@ -278,7 +278,8 @@ fi

# vg
cd ${pangenomeBuildDir}
wget -q https://github.com/vgteam/vg/releases/download/v1.52.0/vg
#wget -q https://github.com/vgteam/vg/releases/download/v1.51.0/vg
wget -q http://public.gi.ucsc.edu/~hickey/vg-patch/vg.98e3b7c867eb64178298535b076189ef7fda5031 -O vg
chmod +x vg
if [[ $STATIC_CHECK -ne 1 || $(ldd vg | grep so | wc -l) -eq 0 ]]
then
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4 changes: 4 additions & 0 deletions src/cactus/cactus_progressive_config.xml
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Expand Up @@ -384,6 +384,8 @@
<!-- odgiDrawOptions: options to odgi draw, used for 2d viz -->
<!-- rindexOptions: options to vg gbwt -r (r-index construction) as used to make haplotype sampling index -->
<!-- haplOptions: options to vg haplotypes as used to make haplotype sampling index -->
<!-- minRGFAFragment: smallest rGFA (rank > 0) cover path to write -->
<!-- keepRGFAFragmentsInChromGraphs: toggle whether rGFA fragments end up in chromosome graphs (by default only in gbz/rgfa) -->
<graphmap_join
gfaffix="1"
clipNonMinigraph="1"
Expand All @@ -396,6 +398,8 @@
odgiDrawOptions="-H 1000"
rindexOptions="-p"
haplOptions="-v 2"
minRGFAFragment="50"
keepRGFAFragmentsInChromGraphs="0"
/>
<!-- hal2vg options -->
<!-- includeMinigraph: include minigraph node sequences as paths in output (note that cactus-graphmap-join will still remove them by default) -->
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