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sicotteh wants to merge 102 commits into from
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Hgvsg #6

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1282f6f
Fix filename in if-condition
dariober Sep 28, 2018
923fd97
Resolved merge conflict by incorporating both suggestions.
Steven-N-Hart Jan 13, 2020
f0018da
Merge remote-tracking branch 'origin/master'
Steven-N-Hart Feb 12, 2020
2818a6b
Fixed inconsistent tabs and spaces
Steven-N-Hart Feb 12, 2020
f5a8d18
fixed some PEP8 violations and an incorrect import when getting prote…
Steven-N-Hart Feb 12, 2020
82fdf37
updated version number, fixed "feature" that silently dropped variant…
Steven-N-Hart Jun 22, 2020
abd587b
line endings and updated release info
Steven-N-Hart Jun 23, 2020
4641f12
Added HGVSc
Steven-N-Hart Jun 23, 2020
ea1d69f
fixed incorrect HGVS INFO filed order.
Steven-N-Hart Jun 23, 2020
da6a0c9
1. No longer drops chromosomes not present in the definition file. (e…
Steven-N-Hart Jul 13, 2020
732af07
using python 3.8.2, had to use newer versions of gevent & six
mcmark-8 Sep 3, 2020
79ff780
Update config_template.txt
Steven-N-Hart Sep 15, 2020
327d660
Update config_template.txt
Steven-N-Hart Sep 15, 2020
ee81136
Updates to get CAVA running in ODP
mcmark-8 Sep 21, 2020
0f9ba23
Added Docker file and README.md
Steven-N-Hart Sep 21, 2020
2cc7e31
Added Docker file and updated README.md
Steven-N-Hart Sep 22, 2020
89def67
fixed parameter error message for normalized_mitochondrial_chrom
mcmark-8 Sep 23, 2020
939b648
allow sorting by M and consider transcripts for chrom 'M'
mcmark-8 Sep 23, 2020
a37215e
Standardized VERSION
Steven-N-Hart Sep 25, 2020
6960c19
added test VCF files
Steven-N-Hart Sep 25, 2020
21f05e9
added test VCF files & procedures
Steven-N-Hart Sep 30, 2020
81fcd94
Merge pull request #13 from Steven-N-Hart/ref_db_build
Steven-N-Hart Sep 30, 2020
c1a847e
Changed instructions for compiling tx.db
Steven-N-Hart Oct 1, 2020
62585d2
Changed instructions for compiling tx.db
Steven-N-Hart Oct 5, 2020
8e49d47
updated tests
Steven-N-Hart Oct 6, 2020
8cbcb23
adding mt normalization
Steven-N-Hart Oct 6, 2020
f57d603
Merge branch 'mane' into update-requirements
Steven-N-Hart Oct 6, 2020
b44013b
fixed line separators
Steven-N-Hart Oct 12, 2020
6fd59d2
Merge pull request #14 from Steven-N-Hart/update-requirements
Steven-N-Hart Oct 12, 2020
2bbeebe
updated version info. Scripts for MANE transcripts.
Steven-N-Hart Oct 12, 2020
a39769c
Better handling of poor VCF files with '*' and non ACTG alts
Steven-N-Hart Oct 19, 2020
a919651
Added option to force the ALTFLAG column creation
mcmark-8 Oct 20, 2020
9e00617
Merge pull request #15 from Steven-N-Hart/option-allow-altflag
Steven-N-Hart Oct 26, 2020
9287f8d
HGVSp addition, also modified CSN to output fsTer rather than fsX. CS…
Nov 2, 2020
3494d8c
Merge pull request #17 from Steven-N-Hart/dev
Steven-N-Hart Nov 2, 2020
90b8f90
merged in most recent master and resolved conflicts. Added @config_te…
Nov 4, 2020
c48c671
clean up prior to checkin
Nov 4, 2020
72ec928
Reverted fixing CSN.. extX will remain extX .. fix it to get HGVSp
Nov 4, 2020
4d997b0
Better handling of poor VCF files with '*' and non ACTG alts
Nov 5, 2020
cdc9327
Moved VERSION info
Nov 5, 2020
6fd27ac
added tabix to docker file
Nov 5, 2020
987cf10
updating MANE to export prteins
Nov 5, 2020
a3d84c1
Moving VERSION file
Nov 5, 2020
6b982bc
Moving VERSION file
Nov 5, 2020
939e72d
All database prep scripts now export the protein in the txt files
Nov 6, 2020
57b5f79
deleting large unecessary files
Nov 6, 2020
abaedd5
HGVSP now reading from text file instead of custom one. Also changed…
Nov 6, 2020
7b3c00c
Hugues tests passing
Nov 6, 2020
896185b
changed shebang
Nov 6, 2020
513dba7
deleting unecessary files
Nov 6, 2020
f3a03d8
removed transcript2protein option
Nov 6, 2020
3e0ecfe
recursion killer
Nov 6, 2020
a1b6fe8
recursion killer
Nov 6, 2020
434d4fb
Final test approval
Nov 6, 2020
79ca709
Added example test files
Nov 6, 2020
ca55376
Merge pull request #19 from Steven-N-Hart/addHGVSforFS
Steven-N-Hart Nov 6, 2020
7b49938
Added flags variables to TSV output processing
mcmark-8 Nov 20, 2020
32ebda6
Added HGVS column headers to TSV output
mcmark-8 Nov 20, 2020
3a104f0
TSV output, column preservation
mcmark-8 Nov 23, 2020
062f97b
Fix for TSV file writing
mcmark-8 Nov 23, 2020
d61eac6
empty HGVSC fields get set to .
mcmark-8 Nov 24, 2020
214ad28
Allow transcript dictionaries with no protein columns
mcmark-8 Nov 25, 2020
7db66e6
incremented CAVA version
mcmark-8 Nov 25, 2020
af8f171
Merge pull request #20 from Steven-N-Hart/dev
Steven-N-Hart Nov 30, 2020
ed0f05b
Updated to allow for alt being "." and "?" in translated sequences
Steven-N-Hart May 13, 2021
8cd00d6
changed path to version file
Steven-N-Hart May 28, 2021
77bb949
bumped version & line terminators
Nov 30, 2020
b456a8a
added .dockerignore file
May 11, 2021
09cdb95
refactored VERSION name search and updated README for db builds
Jun 8, 2021
8351f08
changed line separators
Jun 8, 2021
ea20b9b
Deleted unused files and passed tests
Jun 8, 2021
3e65d1a
PEP8 formatting
Jun 8, 2021
4e408b2
PEP8 formatting
Jun 8, 2021
981fba3
Added most of Hugues changes, new tests
Jun 8, 2021
c4135c8
Added end2end testing
Jun 11, 2021
ff48b03
added process to get test reference data
Jun 13, 2021
cfcddc6
fix import structures
Steven-N-Hart Jun 13, 2021
16bb1ee
e2e test passing
Steven-N-Hart Jun 13, 2021
3a47a35
removed extra configs, reformats
Steven-N-Hart Jun 13, 2021
df59f08
Both tests passed, reformatting, and re-architecting methods from Pyc…
Steven-N-Hart Jun 13, 2021
d4cbfb9
updated README.md
Steven-N-Hart Jun 13, 2021
39a8458
Released on pypi
Steven-N-Hart Jun 13, 2021
a7d7a9e
Fixed locations of database builds
Steven-N-Hart Jun 16, 2021
ce507a5
Added Hugues tests for Met1toAA and EarlyStopInMiddle3BP
Steven-N-Hart Jun 16, 2021
edb77d4
Merge pull request #1 from Steven-N-Hart/dev
Steven-N-Hart Jun 16, 2021
259005d
Reorder
Jun 20, 2021
0ab447f
Merge pull request #2 from Steven-N-Hart/dev
Steven-N-Hart Jun 20, 2021
957934f
Adding support for gVCFs
Steven-N-Hart Jun 25, 2021
e4c29f3
Update mane_db_prep.py
Steven-N-Hart Jul 29, 2021
41c7ac7
Create python-publish.yml
Steven-N-Hart Jul 29, 2021
46dea55
Update VERSION
Steven-N-Hart Jul 29, 2021
ad28642
Merge pull request #4 from Steven-N-Hart/master
Steven-N-Hart Jul 29, 2021
3fd9823
Add back test directory AND allow variants that either straddle the e…
Nov 2, 2021
525390e
push changes for fix HGVS issues
Dec 29, 2021
8f50358
added tests for BRCA1 deletions/insertions right outside the ends and…
Jan 20, 2022
2c27261
another data dir added to .gitignore
Jan 20, 2022
b570a19
temporararely remote file from .gitignore
Jan 20, 2022
6d10c7b
temporararely remote file from .gitignore
Jan 20, 2022
538aa27
add .gitignore after removing large file from history using filter
Jan 20, 2022
33a233f
Fixed bugs around splice site, Methionine. and added 5X speed improve…
Feb 17, 2022
14d6725
Added unit tests, support repeats [] annotations, dna inversions (inv…
Mar 9, 2022
2e9c132
Added CAVA_HGVSg, removing old CAVA annotation, and debugged proper u…
Mar 18, 2022
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Update config_template.txt 
changed default to 1
  • Loading branch information
@Steven-N-Hart
Steven-N-Hart authored Sep 15, 2020
commit 79ff78080b648d828028c06cc01e6bc67e0b541b
2 changes: 1 addition & 1 deletion config_template.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -89,5 +89,5 @@
# 4 = {'AGA':'X'} Mitochondrial Code: changes RAGAX, RAGGX, IAUAM, XUGAW (used if chr == M or MT)
# 5 = {'ATA': 'I'} Bacterial code
# Default = 1
@codon_usage = 4
@codon_usage = 1