I think the current problem with the relationships may be due to running localize_nodes() near the end of the process (mostly as a quick way to get the anchors right). I think this may only add info to the edges, instead of removing it first.
Debugging still in progress.
Tested on chloroplasts datasets: add C_sativus then Z_mays; then remove Z_mays.
Currently export comparison:
TODO:
Lankveld, Thijs van (acf5a6a0) at 31 Mar 14:35
When removing genomes, also try to merge when a color is removed fr...
... and 1 more commit
Lankveld, Thijs van (ef58226c) at 31 Mar 13:50
Adjusted pangenome exporter to write nucleotide (non-0) node freque...
... and 1 more commit
Lankveld, Thijs van (df6f550d) at 30 Mar 14:56
Added checks after removing sequence and genome whether all the rel...
... and 2 more commits
Lankveld, Thijs van (ccbe301c) at 29 Mar 14:45
Removing sequence and genome nodes as well (and update localization).
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Lankveld, Thijs van (9dc9e188) at 27 Mar 11:35
Fully processed test add genomes 1 and 5, remove genome 5.
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Lankveld, Thijs van (a594c58b) at 23 Mar 13:42
Initial implementation of removing genomes from an existing pangenome.
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Lankveld, Thijs van (c484d8bc) at 21 Oct 14:33
Merge branch 'pantools_v3.4' into 'release'
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Notes:
test/
test_code/
removed as its contents were identical to those
in test/
nl.wur.bif.pantools
Lankveld, Thijs van (d4269b01) at 21 Oct 14:31
Merge branch 'release' into 'pantools_v3.4'
... and 18 more commits
Notes:
test/
test_code/
removed as its contents were identical to those
in test/
nl.wur.bif.pantools
Lankveld, Thijs van (a54a27b8) at 21 Oct 14:26
Merge branch 'pantools_v3.2' into 'release'
... and 226 more commits
added compilation information to README.md and added citation information to consensus_tree function
added compilation information to README.md and added citation information to consensus_tree function
Lankveld, Thijs van (e2a57864) at 21 Oct 14:24
Merge branch 'pantools_v3.1' into 'release'
... and 8 more commits