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Ref alt allele #8

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Merged
khetherin merged 57 commits into from
Oct 13, 2025
Merged

Ref alt allele #8

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217ea3f
added a function for adjusting the position
khetherin Sep 19, 2025
dcdc873
added a function for inserting a padded base into REF and ALT
khetherin Sep 19, 2025
249880a
added a function for building IUPAC dictionary
khetherin Sep 19, 2025
3badbf3
added function and tests for converting REF that contains IUPAC codes
khetherin Sep 22, 2025
9cc08f0
add docstring
khetherin Sep 22, 2025
d1b09af
created a file to store all variant types and their symbolic allele.
khetherin Sep 22, 2025
dfbfe5c
created a function to read and store symbolic alleles
khetherin Sep 22, 2025
6c8b75f
edit tests
khetherin Sep 22, 2025
54b1e09
removed test line
khetherin Sep 22, 2025
852a4eb
edits to the symbolic alleles
khetherin Sep 23, 2025
9c12853
added description to the symbolic alleles
khetherin Sep 23, 2025
191aa2c
updated the ALT metainformation lines
khetherin Sep 23, 2025
bc3ab8a
removed duplication in the ALT metainformation lines
khetherin Sep 23, 2025
edfc6be
removed duplication and rearrange in the ALT metainformation lines
khetherin Sep 23, 2025
9a7ed73
added an imprecise variant with a start_range and end_range
khetherin Sep 24, 2025
2cda76e
added test for generate_symbolic_alleles
khetherin Sep 24, 2025
3fd76ff
added changes to support generate_symbolic_alleles
khetherin Sep 24, 2025
31d8a95
edited converting iupac codes, added a function for checking ref alle…
khetherin Sep 25, 2025
77c9c35
minor indentation
khetherin Sep 25, 2025
298a375
minor indentation
khetherin Sep 25, 2025
d48ac48
minor indentation
khetherin Sep 25, 2025
95201cb
tests for check_Ref and get_alt
khetherin Sep 25, 2025
327bc9b
print INFO fields in the VCF file
khetherin Sep 25, 2025
e754770
added VCF metainformation lines to the VCF header
khetherin Sep 25, 2025
bfe3b89
edits made to SVLEN
khetherin Sep 25, 2025
3d7ac3d
edited tests
khetherin Sep 25, 2025
32cc48f
edited test file
khetherin Sep 25, 2025
4d4bbc7
edits test with minor edits
khetherin Sep 25, 2025
1e48884
changed function extract_reference_allele, add_padded_base, get_alt
khetherin Sep 25, 2025
ef4866f
determined what to do with Variant_seq=-
khetherin Sep 26, 2025
2f485a5
remove space
khetherin Sep 26, 2025
726ef5e
added docstring
khetherin Sep 26, 2025
25af956
combined files together: sequence_ontology_symbolic_alleles.tsv and s…
khetherin Sep 30, 2025
3806c8d
removed function generate_angled_bracket
khetherin Sep 30, 2025
ddab135
removed function adjust_pos
khetherin Sep 30, 2025
cc0c40c
edited parameter placed_before in the function add_padded_base
khetherin Sep 30, 2025
37caa38
simplified notation
khetherin Sep 30, 2025
0cce4c6
simplified notation
khetherin Sep 30, 2025
eb3a0c7
removed unused import
khetherin Sep 30, 2025
c5d0325
edit docstring
khetherin Sep 30, 2025
3c265db
edit docstring
khetherin Sep 30, 2025
3ef855b
refactor renaming variables
khetherin Sep 30, 2025
48e2e86
edit printing reserved metainformation string
khetherin Sep 30, 2025
abc9d76
edited svALTkeys.tsv
khetherin Oct 1, 2025
e0c1e45
consolidated reading files into one function: read_file
khetherin Oct 1, 2025
e68890b
added docstring
khetherin Oct 1, 2025
0d61e87
consolidated generating all possible standard structured lines
khetherin Oct 1, 2025
1c6db0e
consolidated all possible lines into one dictionary
khetherin Oct 2, 2025
50fd97e
consolidated standard lines into one dictionary
khetherin Oct 2, 2025
a10b3f7
build the iupac ambiguity dictionary once
khetherin Oct 2, 2025
2327f9c
edit tests
khetherin Oct 2, 2025
51e9324
minor edits
khetherin Oct 2, 2025
c67df45
minor edits
khetherin Oct 2, 2025
47cbaeb
edit test
khetherin Oct 3, 2025
63c3d08
edit docstring
khetherin Oct 3, 2025
d7a7a90
return a string
khetherin Oct 3, 2025
52e10e0
removed print statement
khetherin Oct 9, 2025
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