arkal/Transgene issues and pull requests

#62 - Fix same-codon bug (resolves #61)

Pull Request - State: closed - Opened by arkal over 6 years ago

#61 - New Bug in co-expressed mutants without RNA

Issue - State: closed - Opened by arkal over 6 years ago

#60 - Bug in co-expressed mutants without RNA

Issue - State: closed - Opened by arkal over 6 years ago

#59 - Completely rewrite how fusion junctions are handled

Pull Request - State: closed - Opened by arkal over 6 years ago

#58 - handle RNA-gene acceptors

Issue - State: closed - Opened by arkal over 6 years ago - 1 comment

#57 - Cherry pick from master

Pull Request - State: closed - Opened by arkal over 6 years ago

#56 - Fix logic error in read_fusions (resolves #53)

Pull Request - State: closed - Opened by arkal over 6 years ago

#55 - Fix neg strand deletion edge case (resolves #52)

Pull Request - State: closed - Opened by arkal over 6 years ago

#54 - Fix edge case in indels in repetitive regions (resolves #51)

Pull Request - State: closed - Opened by arkal over 6 years ago

#53 - transgene always rejects fusions with chrM in second partner

Issue - State: closed - Opened by arkal over 6 years ago

#52 - Fix edge case in deletions on the negative strand

Issue - State: closed - Opened by arkal almost 7 years ago

#51 - Fix edge case in indels in repetitive regions

Issue - State: closed - Opened by arkal almost 7 years ago

#50 - Fix bug with synonymous mutation in incomplete transcript (resolves #49)

Pull Request - State: closed - Opened by arkal almost 7 years ago

#49 - Fix bug with Synonymous SNVS and incomplete transcripts

Issue - State: closed - Opened by arkal almost 7 years ago

#48 - Fix bug in snvs touching same codon (resolves #47)

Pull Request - State: closed - Opened by arkal almost 7 years ago

#47 - Fix error in SNVs affecting same codon

Issue - State: closed - Opened by arkal almost 7 years ago

#46 - make a manual/readme

Issue - State: open - Opened by arkal almost 7 years ago

#45 - Implement support for snpeff 4.0+ and VEP (Resolves #44)

Pull Request - State: closed - Opened by arkal almost 7 years ago

#44 - support for snpeff 4.0+ and vep

Issue - State: closed - Opened by arkal almost 7 years ago

#43 - Fix bugs introduced by indel support (resolves #41, resolves #42)

Pull Request - State: closed - Opened by arkal about 7 years ago

#42 - Fix bug in indels using wrong first exon coords

Issue - State: closed - Opened by arkal about 7 years ago

#41 - Fix pseudo-mnp support broken by indels

Issue - State: closed - Opened by arkal about 7 years ago

#40 - support for MNPS

Issue - State: open - Opened by arkal about 7 years ago

#39 - Make test files use git lfs

Issue - State: open - Opened by arkal about 7 years ago

#38 - Add VAF info to IAR name (resolves #37)

Pull Request - State: closed - Opened by arkal about 7 years ago

#37 - add vaf information to IAR

Issue - State: closed - Opened by arkal about 7 years ago

#36 - Add indel support (resolves #30)

Pull Request - State: closed - Opened by arkal about 7 years ago

#35 - Filter fusion artifacts (resolves #29)

Pull Request - State: closed - Opened by arkal about 7 years ago

#34 - Handle Multi Allelic Variants (resolves #33)

Pull Request - State: closed - Opened by arkal about 7 years ago

#33 - Handle multiallelic variants

Issue - State: closed - Opened by arkal about 7 years ago

#32 - Fix bug in bam parsing that misprocessed low qual mutants (resolves #31)

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

#31 - Fix bug allowing low qual mutants to pass

Issue - State: closed - Opened by arkal over 7 years ago

#30 - handle indels

Issue - State: closed - Opened by arkal over 7 years ago

#29 - Filter fusion artefacts

Issue - State: closed - Opened by arkal over 7 years ago

#28 - Add error log for no actionable mutations (resolves #27)

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

#27 - Add error line to logfile for no actionable

Issue - State: closed - Opened by arkal over 7 years ago

#26 - Properly handle lack of non synonymous mutations (resolves #25)

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

#25 - Raise no actionalbe mutations if zero peptides in output

Issue - State: closed - Opened by arkal over 7 years ago

#24 - Skip malformed fusions (resolves #23)

Pull Request - State: closed - Opened by jpfeil over 7 years ago - 1 comment

#23 - Skip malformed fusion products

Issue - State: closed - Opened by jpfeil over 7 years ago

#22 - Add to pypi

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

#21 - Add GENCODE revisions to fusions (resolves #20)

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

#20 - Ensure Transgene spits out GENCODE revisions for fusions

Issue - State: closed - Opened by arkal almost 8 years ago - 3 comments

#19 - Implement OxoG filtering support (resolves #13)

Pull Request - State: closed - Opened by arkal almost 8 years ago

#18 - Fix snpeff n+1 issue (resolves #16)

Pull Request - State: closed - Opened by arkal almost 8 years ago

#17 - Fix snpeff n+1 issue (resolves #16)

Pull Request - State: closed - Opened by arkal almost 8 years ago

#16 - Fix snpeff n+1 error

Issue - State: closed - Opened by arkal almost 8 years ago

#15 - Fix fusion alignment file error (resolves #14)

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

#14 - Fix missing fusion alignment file error

Issue - State: closed - Opened by jpfeil almost 8 years ago

#13 - Add Oxo-G filtering option

Issue - State: closed - Opened by arkal almost 8 years ago

#12 - Add support for new gencode peptide fasta header (resolves #11)

Pull Request - State: closed - Opened by arkal almost 8 years ago

#11 - Add support for new gencode format

Issue - State: closed - Opened by arkal almost 8 years ago

#10 - Add fusion support (resolves #1)

Pull Request - State: closed - Opened by jpfeil almost 8 years ago - 4 comments

#9 - Emit normal peptides (resolves #8)

Pull Request - State: closed - Opened by arkal over 8 years ago

#8 - Emit normal peptides

Issue - State: closed - Opened by arkal over 8 years ago

#7 - Add fusion test

Issue - State: closed - Opened by jpfeil over 8 years ago

#6 - Add unit tests (resolves #5)

Pull Request - State: closed - Opened by jpfeil over 8 years ago - 3 comments

#5 - Add unit tests

Issue - State: closed - Opened by jpfeil over 8 years ago

#4 - Emit a processed vcf

Issue - State: closed - Opened by arkal over 8 years ago - 1 comment

#3 - Add filtering by RNA-seq

Issue - State: closed - Opened by arkal over 8 years ago - 1 comment

#2 - Add fusion support (resolves #1)

Pull Request - State: closed - Opened by jpfeil over 8 years ago - 12 comments
Labels: needs work

#1 - Add fusion support

Issue - State: closed - Opened by jpfeil over 8 years ago - 1 comment

GitHub / arkal/Transgene issues and pull requests