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Dear sir,
Using Anchorwave-cactus, we have successfully constructed a graph-based pangenome from 97 samples. However, the centromeric region is proving to be quite confusing and is impeding the use of the 'vg autoindex' command. To address this issue, we intend to remove this particular region.
The following image depicts two chromosomes.
The results of odgi extract are also abnormal,for example,
complex region
#path start end
001_111#0#Chr4 19375679 19375685
001_111#0#Chr4 19377065 19377092
001_111#0#Chr4 19395332 19395353
001_111#0#Chr4 19396674 19396680
001_111#0#Chr5 19250513 19250523
P 001_111#0#Chr4:19375685-22740591
P 001_111#0#Chr4:0-19377065
P 001_111#0#Chr4:19377092-22740591
P 001_111#0#Chr4:0-19395332
P 001_111#0#Chr4:19395353-22740591
P 001_111#0#Chr4:0-19396674
P 001_111#0#Chr4:19396680-22740591
P 001_111#0#Chr5:0-19250513
P 001_111#0#Chr5:19250523-30923699
The results show that chr 5 of 001_111 is correct, but the results for chr 4 are incorrect.
Here is the command I used
Dear sir,
Using Anchorwave-cactus, we have successfully constructed a graph-based pangenome from 97 samples. However, the centromeric region is proving to be quite confusing and is impeding the use of the 'vg autoindex' command. To address this issue, we intend to remove this particular region.
The following image depicts two chromosomes.
The result joint-clip.P_C97.gfa have no path or Walk, is that normal?
Does odgi support drawing the cliped or pruned graph ?
log file
odgi: /home/hickey/dev/cactus/build/bin-tmp/cactus/build-pangenome-tools/odgi-v0.8.3/build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/int_vector.hpp:1360: sdsl::int_vector< >::reference sdsl::int_vector< >::operator[](const size_type&) [with unsigned char t_width = 1; sdsl::int_vector< >::reference = sdsl::int_vector_reference<sdsl::int_vector<1> >; sdsl::int_vector< >::size_type = long unsigned int]: Assertion `idx < this->size()' failed.
/var/spool/pbs/mom_priv/jobs/903065.mn01.SC: line 22: 25972 Aborted (core dumped) odgi layout -i joint-clip.P.sort.og -o graphs.combined.og.lay -T graphs.combined.og.lay.tsv -t 30 -P
/var/spool/pbs/mom_priv/jobs/903065.mn01.SC: line 23: 26685 Segmentation fault (core dumped) odgi draw -i joint-clip.P.sort.og -c graphs.combined.og.lay -p graphs.combined.og.lay.draw.png -H 1000
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