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Fix wrong coordinate from genomic indels, Fix no ref/alt errors. Add genePred support to allow users to easily load their own transcripts #54

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Fix wrong coordinate from genomic indels, Fix no ref/alt errors. Add genePred support to allow users to easily load their own transcripts #54

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e65db83
Patch on top of latest counsyl/hgvs - indel resolution. Load genePred…
davmlaw Mar 16, 2020
e2f7dfb
Unit tests for previously failing HGVS names
davmlaw Mar 16, 2020
9ffdc7f
Populate alt for values like NC_000001.11:g.169549811=
davmlaw Apr 22, 2020
00a2205
Support mito (ie "m.")
davmlaw Apr 29, 2020
2b4ac8b
Revert "Support mito (ie "m.")"
davmlaw Apr 29, 2020
a6e238e
Support n. (non-coding) ie https://github.com/counsyl/hgvs/issues/7
davmlaw May 12, 2021
957d25c
Make sure non-coding doesn't have 5' or 3' UTR offsets
davmlaw Sep 7, 2021
1a8b67f
Refactor - move functions into methods
davmlaw Oct 12, 2021
67ab67f
Start of cDNA matching code changes. Put everything through 1 path as…
davmlaw Oct 12, 2021
04ac8a7
Handle gaps
davmlaw Oct 13, 2021
ae264c1
Handle gaps - put back exons as we need them to work out flanking
davmlaw Oct 13, 2021
5a4b48b
checkpoint - handle flanking
davmlaw Oct 14, 2021
5667511
Finish off gap handling code
davmlaw Oct 14, 2021
c1f2099
linting
davmlaw Oct 14, 2021
dc6d638
Keep module interface the same
davmlaw Oct 15, 2021
0d6ddd5
Better errors, note about not using single=True
davmlaw Oct 15, 2021
79fa49b
Keep module interface the same
davmlaw Oct 15, 2021
2145f96
Don't die in gaps when going the other way. Change testing data
davmlaw Oct 15, 2021
d58789b
Always use cDNA as exons, to handle those strange cases like eg NM_00…
davmlaw Oct 15, 2021
2dbd69d
Make sure to include models in package
davmlaw Oct 18, 2021
4271aa7
Better error message
davmlaw Oct 22, 2021
cc3de4d
Data generation scripts
davmlaw Oct 22, 2021
2e71ba9
Keep track of what other contigs we have coordinates for (eg chrX and…
davmlaw Oct 27, 2021
1337350
For non-coding, PyHGVS has cds_start = end not start (so coding lengt…
davmlaw Oct 28, 2021
6c5e381
Use transcript offsets rather than exon lengths so we handle gaps pro…
davmlaw Nov 10, 2021
2ca3e08
Simplify and make consistent
davmlaw Nov 10, 2021
b4571a7
Previous change didn't work on negative strand
davmlaw Nov 10, 2021
bb17f43
Make sure exons are sorted correctly
davmlaw Nov 10, 2021
dbc621f
Support LRG transcripts (was setting as gene not transcripts if no ge…
davmlaw Nov 15, 2021
1409aba
Use ref for alt on any reference HGVS
davmlaw Nov 16, 2021
9ceb649
Validate coordinate span and reference are the same, as eg c.1727_174…
davmlaw Nov 16, 2021
27535c3
Support mitochondria
davmlaw Nov 16, 2021
a0a8edd
Bump version so I can track it
davmlaw Nov 24, 2021
12924f0
HGVS issue #61 - Reference HGVS without reference base leads to wrong…
davmlaw Dec 9, 2021
70565eb
Bump version, add changelog
davmlaw Dec 9, 2021
1ea73ad
Use same code for calculating transcript position of start/stop codon…
davmlaw Jan 14, 2022
f42bd06
Changelog
davmlaw Jan 14, 2022
d59d079
No need to sort before storing as we don't rely on order and re-sort …
davmlaw Jan 14, 2022
eef2514
Including coding start/end transcript coords if available
davmlaw Jan 14, 2022
936d276
Fix syntax error
davmlaw Jan 17, 2022
992c4af
Fix issue where dups always matched ref allele
davmlaw Aug 1, 2022
de3a1d3
Generating transcripts is now handled via https://github.com/SACGF/cdot
davmlaw Aug 18, 2022
715c4f2
Support for coord range + equals ie "NC_000010.10:g.89623915_89623920="
davmlaw Apr 12, 2023
116217d
Bump version
davmlaw Apr 12, 2023
7591c13
#57 - c. dup converted back to delins
davmlaw May 25, 2023
8b30efd
bump version
davmlaw Jun 1, 2023
ef00572
Use min of 100 again for normalization window space
davmlaw Jun 14, 2023
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14 changes: 14 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,19 @@
# HGVS library change log

## Unreleased
- Use same code for calculating transcript position of start/stop codons.
- Be able to pass in pre-calculated start/stop from transcript_json if available

## 0.12.1 (2021-12-09)
- Fix issue #61 - Regex for reference HGVS without reference base

## 0.12.0 (2021-11-24)
- cDNA gaps
- Refactor models
- Support non-coding, mitochondria and LRG transcripts
- Validate coordinate span equals reference length
- Scripts to generate transcripts from RefSeq and Ensembl GTFs on the web

## 0.9.2 (2014-12-11)
- Rename package to pyhgvs to avoid naming conflict with other libraries.

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