J35P312/SVDB issues and pull requests

#69 - List index out of range

Issue - State: open - Opened by gavinmonahan about 1 year ago - 1 comment

#68 - fixed typo

Pull Request - State: closed - Opened by bounlu about 1 year ago

#67 - Only keep one INFO field

Issue - State: open - Opened by Akazhiel almost 2 years ago - 1 comment

#66 - UnicodeDecodeError

Issue - State: closed - Opened by yangyxt almost 2 years ago - 3 comments

#65 - Fix argument mismatch

Pull Request - State: closed - Opened by ramprasadn almost 2 years ago - 5 comments

#64 - main() takes exactly 2 positional arguments (1 given)

Issue - State: closed - Opened by FriederikeHanssen almost 2 years ago - 1 comment

#63 - Syntax error with singularity image

Issue - State: closed - Opened by yangyxt almost 2 years ago - 2 comments

#62 - update tmp file names

Pull Request - State: closed - Opened by ramprasadn about 2 years ago - 3 comments

#61 - 2.7.0

Pull Request - State: closed - Opened by J35P312 about 2 years ago

#60 - How to combine delly,lumpy,manta and tiddit result?

Issue - State: closed - Opened by ld9866 about 2 years ago - 5 comments

#59 - set=Intersection is not fully informative; add FOUND_IN tag?

Issue - State: open - Opened by dnil about 2 years ago - 2 comments

#58 - Enhance the FORMAT column of merge subcommand.

Issue - State: open - Opened by xiucz about 2 years ago - 1 comment

#57 - The install document should be updated.

Issue - State: closed - Opened by xiucz about 2 years ago - 2 comments

#56 - Using SVDB for merging VCF files of different samples?

Issue - State: closed - Opened by dr-ashu-geno about 2 years ago - 1 comment

#55 - Merging BNDs in different chromosomes

Issue - State: closed - Opened by fgvieira about 2 years ago - 3 comments

#54 - Parsing multiple filters

Pull Request - State: closed - Opened by jemten over 2 years ago

#53 - places svdb_origin tag under if statement

Pull Request - State: closed - Opened by jemten over 2 years ago - 1 comment

#52 - Find sv from seq

Pull Request - State: closed - Opened by J35P312 over 2 years ago - 1 comment

#51 - Bug: missing headers

Issue - State: open - Opened by fgvieira over 2 years ago

#50 - Feat/fix picarderror

Pull Request - State: closed - Opened by ramprasadn over 2 years ago - 2 comments

#49 - Fixed python import issue with python3

Pull Request - State: closed - Opened by insung3511 over 2 years ago - 6 comments

#48 - Add information for all callers in INFO for overlapping events

Pull Request - State: closed - Opened by J35P312 over 2 years ago - 3 comments

#47 - Add missing header infomation in svdb query output

Pull Request - State: closed - Opened by ramprasadn over 2 years ago - 2 comments

#46 - Add information for all callers in `INFO` for overlapping events

Issue - State: closed - Opened by khurrammaqbool over 2 years ago - 1 comment

#45 - Enable svdb query for multiple databases

Pull Request - State: closed - Opened by ramprasadn over 2 years ago - 2 comments

#44 - updating dockerfile

Pull Request - State: closed - Opened by jemten over 2 years ago - 2 comments

#43 - fix: BND position

Pull Request - State: closed - Opened by khurrammaqbool over 2 years ago - 1 comment

#42 - No_intra flag

Issue - State: closed - Opened by Akazhiel almost 3 years ago - 1 comment

#41 - changed breakend reading

Pull Request - State: closed - Opened by kristinebilgrav about 3 years ago - 1 comment

#40 - Insertion distance

Pull Request - State: closed - Opened by J35P312 about 3 years ago - 1 comment

#39 - Quickfixes to the export module

Pull Request - State: closed - Opened by J35P312 almost 4 years ago - 1 comment

#38 - Test DBSCAN and overlap modules

Pull Request - State: closed - Opened by J35P312 almost 4 years ago - 1 comment

#37 - Initial tests

Pull Request - State: closed - Opened by DanielAndreasen almost 4 years ago - 2 comments

#36 - Cleanup

Pull Request - State: closed - Opened by DanielAndreasen almost 4 years ago - 6 comments

#35 - Refactoring

Issue - State: open - Opened by DanielAndreasen almost 4 years ago - 5 comments

#34 - Add new variants to existing database

Issue - State: open - Opened by DanielAndreasen almost 4 years ago - 1 comment

#33 - What does the frequency mean?

Issue - State: closed - Opened by DanielAndreasen about 4 years ago - 2 comments

#32 - Query: Implement max_frq in order to avoid higher frequencies SVs

Pull Request - State: closed - Opened by DanielAndreasen over 4 years ago - 1 comment

#31 - Query: Only write variants with frequency lower than a given value

Issue - State: closed - Opened by DanielAndreasen over 4 years ago - 1 comment

#30 - More readable layout of README

Pull Request - State: closed - Opened by DanielAndreasen over 4 years ago - 1 comment

#29 - feat(docker): adds a dockerfile

Pull Request - State: closed - Opened by jemten over 4 years ago - 1 comment

#28 - Query is failing with UnicodeDecodeError

Issue - State: closed - Opened by hassanfa over 4 years ago - 1 comment

#27 - Option to disable "Intersection" in set field

Issue - State: closed - Opened by bjhall over 4 years ago - 5 comments

#26 - What do "filterIn" "FilteredInAll" and "Intersection" mean in set flag?

Issue - State: closed - Opened by YiweiNiu over 4 years ago - 2 comments

#25 - Update LICENSE

Pull Request - State: closed - Opened by dnil almost 5 years ago - 1 comment

#24 - Add option to only include PASS SVs when building DB

Issue - State: closed - Opened by fgvieira about 5 years ago - 1 comment

#23 - Error when exporting database

Issue - State: closed - Opened by fgvieira about 5 years ago - 2 comments

#22 - User defined VCF header

Issue - State: open - Opened by fgvieira about 5 years ago

#21 - Error when quering custom database

Issue - State: closed - Opened by fgvieira about 5 years ago - 2 comments

#20 - Keep sample (genotype) information

Issue - State: closed - Opened by fgvieira about 5 years ago - 3 comments

#19 - Include all SV IDs on the merged ID

Issue - State: closed - Opened by fgvieira about 5 years ago - 1 comment

#18 - Support for bgzip VCF files

Issue - State: closed - Opened by fgvieira about 5 years ago - 1 comment

#17 - svdb merge changes VCF header

Issue - State: open - Opened by Thatguy027 about 6 years ago - 1 comment

#16 - Double entries from merge command

Issue - State: open - Opened by Thatguy027 over 6 years ago - 10 comments

#15 - Python 3 compatibility

Issue - State: closed - Opened by holtgrewe over 6 years ago - 5 comments

#14 - Interpretation of genotype counts

Issue - State: closed - Opened by holtgrewe over 6 years ago - 2 comments

#13 - Bioconda package

Issue - State: closed - Opened by holtgrewe over 6 years ago - 2 comments

#12 - Clarify license

Issue - State: closed - Opened by holtgrewe over 6 years ago - 2 comments

#11 - No match in db, do not add to vcf file

Issue - State: closed - Opened by henrikstranneheim about 7 years ago - 1 comment

#10 - More generic information extraction in svdb query

Issue - State: open - Opened by henrikstranneheim over 7 years ago - 1 comment

#9 - svdb query error using decipher db

Issue - State: closed - Opened by henrikstranneheim over 7 years ago - 3 comments

#8 - version

Issue - State: closed - Opened by henrikstranneheim over 7 years ago - 3 comments

#7 - Add command to vcf header

Issue - State: closed - Opened by henrikstranneheim over 7 years ago - 1 comment

#6 - Use priotag instead of filename in INFO field

Issue - State: closed - Opened by henrikstranneheim over 7 years ago - 1 comment

#5 - Add sv caller tag to vcf input parameter and prio flag

Issue - State: closed - Opened by henrikstranneheim over 7 years ago - 1 comment

#4 - Nicely done!

Pull Request - State: closed - Opened by J35P312 over 7 years ago

#3 - Fix mistyped header

Pull Request - State: closed - Opened by marcelm almost 8 years ago - 2 comments

#2 - Fix cythonize and imports

Pull Request - State: closed - Opened by marcelm almost 8 years ago - 1 comment

#1 - Make SVDB pip-installable

Pull Request - State: closed - Opened by marcelm almost 8 years ago - 1 comment

GitHub / J35P312/SVDB issues and pull requests