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Uncertain ranges #699

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Uncertain ranges #699

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5054739
Support indefinite and definite uncertain ranges, and unbalanced unce…
theferrit32 Sep 20, 2023
1f624ad
Rebuild hgvs grammar due to whitespace changes
theferrit32 Sep 20, 2023
2bcccc2
Merge branch 'main' into 225-uncertain-ranges
andreasprlic Dec 11, 2023
722b142
Merge branch '712-fix-dev-install' into 225-uncertain-ranges
andreasprlic Dec 11, 2023
c15c552
feat(test): minor addition to test to make sure the breakpoints are u…
andreasprlic Dec 11, 2023
8a4341a
feat(g_to_c): this adds support for g_to_c of uncertain coordinates. …
andreasprlic Dec 12, 2023
1983654
Merge branch 'main' into 225-uncertain-ranges
andreasprlic Dec 12, 2023
2e4ae22
update CODEOWNERS to @biocommons/maintainers
reece Jan 19, 2024
82d7331
use shared stale action configuration
reece Jan 31, 2024
a045165
import and standardize issue templates from biocommons.example
Jan 31, 2024
43a556c
add standardized github labels and update action
Jan 31, 2024
3ea0c5c
expose clearer name for label sync action
Jan 31, 2024
1e2a433
remove .github/ISSUE_TEMPLATE (in order to use templates in .github r…
Feb 1, 2024
0c4c5d7
migrate to endbug/label-sync with biocommons-wide label config
Feb 1, 2024
4a44582
#688 - remove __future__ usage
davmlaw Feb 7, 2024
6056847
#695 - Remove top level code environment scripts from modules
davmlaw Feb 9, 2024
cce1c6f
update stale action to use stale.yml from worfklow-template
Feb 13, 2024
261245a
feat(imprecise hgvs_c): adding support to create imprecise hgvs_c s.
andreasprlic Feb 20, 2024
52adbe9
Merge branch 'main' into 225-uncertain-ranges
andreasprlic Feb 20, 2024
609244a
feat(imprecise g_to_c): g_to_c now works. c_to_g not working yet. Req…
andreasprlic Feb 21, 2024
0364f37
feat(cleanup): removing broken c_to_g unit test for imprecise events.
andreasprlic Feb 24, 2024
4c7ecbf
Simplify parser to use None for single-digit intervals. Fixed format …
theferrit32 Mar 11, 2024
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7 changes: 6 additions & 1 deletion src/hgvs/_data/hgvs.pymeta
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Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,7 @@ pro_ident = '=' -> hgvs.edit.AARefAlt(ref='',alt=''

# potentially indefinite/uncertain intervals
c_interval = def_c_interval | '(' def_c_interval:iv ')' -> iv._set_uncertain()
g_interval = def_g_interval | '(' def_g_interval:iv ')' -> iv._set_uncertain()
g_interval = def_g_uncertain_interval:iv | ('(' def_g_interval:iv ')' -> iv._set_uncertain()) | def_g_interval
m_interval = def_m_interval | '(' def_m_interval:iv ')' -> iv._set_uncertain()
n_interval = def_n_interval | '(' def_n_interval:iv ')' -> iv._set_uncertain()
p_interval = def_p_interval | '(' def_p_interval:iv ')' -> iv._set_uncertain()
Expand All @@ -136,6 +136,11 @@ def_r_interval = (r_pos:start '_' r_pos:end -> hgvs.location.Interval(start,end)
def_c_interval = (c_pos:start '_' c_pos:end -> hgvs.location.BaseOffsetInterval(start,end)) | (c_pos:start -> hgvs.location.BaseOffsetInterval(start,copy.deepcopy(start)))
def_n_interval = (n_pos:start '_' n_pos:end -> hgvs.location.BaseOffsetInterval(start,end)) | (n_pos:start -> hgvs.location.BaseOffsetInterval(start,copy.deepcopy(start)))

# indefinite ranges
def_g_uncertain_interval = '(' def_g_interval:ivl_start ')' '_' '(' def_g_interval:ivl_end ')' -> hgvs.location.Interval(start=ivl_start._set_uncertain(), end=ivl_end._set_uncertain())
| def_g_interval:ivl_start '_' '(' def_g_interval:ivl_end ')' -> hgvs.location.Interval(start=ivl_start._set_uncertain(), end=ivl_end._set_uncertain())
| '(' def_g_interval:ivl_start ')' '_' def_g_interval:ivl_end -> hgvs.location.Interval(start=ivl_start._set_uncertain(), end=ivl_end._set_uncertain())

# positions
c_pos = def_c_pos #| '(' def_c_pos:pos ')' -> pos._set_uncertain()
g_pos = def_g_pos #| '(' def_g_pos:pos ')' -> pos._set_uncertain()
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