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d291aa8546d12be2611313bf02d71da024fa5200
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pinyili2
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3
Make new cadnano reader a bit faster
Merge branch 'master' into pinyili2
Add utility for converting crossovers to types other than intrahelical
Use graph methods to compute location of bead in _other_ segments for better performance; update some development logger messages
Add cadnano vhelix and z_idx information via callbacks in new list-based reader
Fix bug when in new model_from_lists option when setting default nucleotide_rank
remove oxlibs
Merge branch 'master' into pinyili2
Make generate_bead_model use one_bead_per_monomer=True by default with max 1 bead per nt and bp, otherwise False
Draft routine for updating reader list coordinates and orientations
Merge remote-tracking branch 'refs/remotes/origin/pinyili2' into pinyili2
Order of double-stranded segment creation and ds-segment direction should match original cadnano reader.
Fix segment orientation and coordinate splines for new cadnano reader
Delete segmentmodel_from_oxdna.py.bak
Merge branch 'master' into pinyili2
Segmend.connect_ends(...) will not make a crossover for '5prime' locations
Fix bug handling insertions and skips at strand ends; handle multiple consecutive skips; in model_from_lists, convert terminal_crossover dsDNA-dsDNA connections to intrahelical when nearby crossovers exist between the two segments
rename oxdna_pinyi to oxdna
modify bak
remove dot files
remove tests
modify git ignore
remove baks
remove nfs
fix some bugs
set one bead per mono back to False
reset index warning
update one_bead_per_monomer to true
add cite for tacoxdna
update readme
write gitignore
add
re
add
add
a
remove redundant files
add
add
add
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