Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / openvax/isovar issues and pull requests

#123 - Use another genome/annotation?

Issue - State: open - Opened by dining-philosopher over 3 years ago

#121 - added top_gene_name to IsovarResult and removed python 2.7 from Travis

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

#120 - RNA sequencing coverage

Issue - State: open - Opened by nknewnew almost 5 years ago

#119 - WIP: Create mutant protein sequence object

Pull Request - State: closed - Opened by iskandr about 5 years ago

#118 - get more than the top protein sequence

Issue - State: open - Opened by drna over 5 years ago - 1 comment

#117 - Add subsequence method ProteinSequence

Pull Request - State: closed - Opened by iskandr over 5 years ago - 1 comment

#116 - Weird chromosome bug in MT variant under GRCh38

Issue - State: open - Opened by iskandr over 5 years ago

#115 - Faster assembly

Pull Request - State: closed - Opened by iskandr over 5 years ago

#114 - Fix mismatch count after variant

Pull Request - State: closed - Opened by iskandr over 5 years ago - 1 comment

#113 - Multiple phasing types

Pull Request - State: closed - Opened by iskandr over 5 years ago

#112 - Normalize counts by number of mapped reads to get CPM

Issue - State: open - Opened by iskandr over 5 years ago

#111 - Speed up locus read construction

Pull Request - State: closed - Opened by iskandr over 5 years ago

#108 - added module for explicit phasing of somatic phasing

Pull Request - State: closed - Opened by iskandr over 5 years ago

#107 - Exit early if no reference contexts for variant

Pull Request - State: closed - Opened by iskandr over 5 years ago

#105 - use varcode's effects() helper to get handling of intergenic effects

Pull Request - State: closed - Opened by iskandr over 5 years ago - 1 comment

#104 - Major rewrite to enable use of newer pysam, fix several bugs, and add filtering options

Pull Request - State: closed - Opened by iskandr almost 6 years ago - 1 comment

#103 - Threshold ratio of alt alleles to all other non-ref alleles

Issue - State: closed - Opened by iskandr about 6 years ago - 1 comment

#102 - Count read names and not just reads

Issue - State: closed - Opened by iskandr about 6 years ago

#101 - Isovar with pysam > 0.9.0

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

#100 - Constructing wildtype peptides

Issue - State: open - Opened by felixfrenkel over 6 years ago - 3 comments

#99 - Variant sequence ... shorter than min allowed

Issue - State: open - Opened by gilhornung over 6 years ago

#98 - Run integration tests

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

#97 - make all the CLI tools use the same logic for generating/parsing output args

Pull Request - State: closed - Opened by iskandr almost 7 years ago - 1 comment

#96 - Refactor CLI

Pull Request - State: closed - Opened by iskandr almost 7 years ago - 1 comment

#95 - setup error: No such file or directory: 'isovar/__init__.py'

Issue - State: closed - Opened by gilhornung almost 7 years ago - 4 comments

#94 - option --use-duplicate-reads is ignores by isovar-protein-sequences.py

Issue - State: closed - Opened by drna almost 7 years ago - 1 comment

#93 - ASE for Synonymous + Non-synonymous Variants

Issue - State: open - Opened by JPFinnigan almost 7 years ago - 3 comments

#92 - No exon_id in mouse mm9 ensembl annotaiotn

Issue - State: open - Opened by weizhu365 almost 7 years ago

#91 - Isovar on multiple .bam

Issue - State: open - Opened by JPFinnigan about 7 years ago - 1 comment

#90 - Unexpectedly short protein sequences

Issue - State: open - Opened by iskandr about 7 years ago - 9 comments

#89 - Too slow running isovar. Could it be run in multithread?

Issue - State: open - Opened by Jemimacat over 7 years ago

#88 - Questions about Isovar

Issue - State: open - Opened by iskandr over 7 years ago

#87 - User wants "hg19" as genome option

Issue - State: open - Opened by iskandr over 7 years ago

#86 - By default, removing soft-clipped bases.

Pull Request - State: closed - Opened by julia326 over 7 years ago - 2 comments

#85 - AssertionError deep in the stack

Issue - State: closed - Opened by julia326 over 7 years ago - 2 comments

#83 - Fix variant reading into intron

Pull Request - State: closed - Opened by julia326 over 7 years ago - 4 comments

#82 - Exception when deletion extends beyond exon boundary

Issue - State: closed - Opened by julia326 over 7 years ago

#81 - Variant effect has a null `aa_mutation_start_offset`

Issue - State: open - Opened by julia326 almost 8 years ago - 1 comment

#80 - Locus read rewrite

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

#79 - Left align indels

Issue - State: open - Opened by iskandr about 8 years ago

#78 - Exposing --include-mismatches-after-variant as a translation flag.

Pull Request - State: closed - Opened by julia326 about 8 years ago - 1 comment

#77 - Expose flag to include mismatches after the variant

Issue - State: closed - Opened by julia326 about 8 years ago

#76 - Incrementing the minor version, after the mismatches-after-variant change

Pull Request - State: closed - Opened by julia326 about 8 years ago - 2 comments

#75 - Cut a new release

Issue - State: closed - Opened by julia326 about 8 years ago

#74 - Optionally filter by number of mismatches after the variant

Pull Request - State: closed - Opened by julia326 about 8 years ago - 2 comments

#73 - Count mismatches after variant toward total

Issue - State: closed - Opened by julia326 about 8 years ago - 1 comment

#72 - Make phasing of multiple variants on a read explicit (group reads into phase groups)

Issue - State: open - Opened by ihodes about 8 years ago - 4 comments
Labels: bug, enhancement

#71 - Death to namedtuple base classes

Pull Request - State: closed - Opened by iskandr about 8 years ago - 5 comments

#70 - Changed VariantSequence.combine to return None instead of raising exception

Pull Request - State: closed - Opened by iskandr about 8 years ago - 2 comments

#69 - Verify that we de-duplicate identical reads

Issue - State: open - Opened by ihodes about 8 years ago
Labels: question

#68 - Fix assembly and add min alt rna reads

Pull Request - State: closed - Opened by julia326 about 8 years ago - 6 comments

#67 - added --min-alt-rna-reads option

Pull Request - State: closed - Opened by iskandr over 8 years ago - 12 comments

#66 - Elongate coding sequences using reference transcripts

Issue - State: open - Opened by iskandr over 8 years ago
Labels: enhancement

#65 - CLI option `--cosmic_vcf_filename` should use dashes and not underscores

Issue - State: closed - Opened by iskandr over 8 years ago
Labels: refactor

#63 - Travis caching still not working

Issue - State: open - Opened by iskandr over 8 years ago - 1 comment
Labels: bug

#62 - ValueError: Reference genome 'hg19' not found

Issue - State: closed - Opened by ggrimes over 8 years ago - 6 comments

#61 - Trim variant sequences by coverage when matching to reference

Pull Request - State: closed - Opened by iskandr over 8 years ago - 16 comments

#60 - Refactor translation module + translation using mitochondrial genetic code

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

#59 - Merge overlapping read pairs into single LocusRead

Issue - State: open - Opened by iskandr over 8 years ago - 1 comment

#57 - overlap assembly and coverage trimming to create VariantSequence candidates

Pull Request - State: closed - Opened by iskandr over 8 years ago - 1 comment

#56 - Premature length filtering of VariantSequences results in dropped ProteinSequences

Issue - State: closed - Opened by iskandr over 8 years ago - 2 comments
Labels: bug

#55 - Isovar undercounting supporting reference reads

Issue - State: open - Opened by ihodes over 8 years ago - 6 comments
Labels: bug

#54 - Move "scripts" into a real CLI/module/app

Issue - State: closed - Opened by ihodes over 8 years ago
Labels: enhancement

#53 - Fix logging.conf loading

Pull Request - State: closed - Opened by julia326 over 8 years ago - 1 comment

#52 - Error running isovar-variant-sequences.py

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

#51 - Results of isovar-protein-sequences.py no longer printed to screen

Issue - State: closed - Opened by iskandr over 8 years ago - 4 comments

#50 - CLI switch for changing logging levels (not just writing to a file)

Issue - State: open - Opened by ihodes over 8 years ago - 1 comment
Labels: enhancement

#48 - Upping release (0.2.3 -> 0.2.4) to fix bad PyPI formatting

Pull Request - State: closed - Opened by julia326 over 8 years ago - 2 comments

#47 - One logger per module

Pull Request - State: closed - Opened by julia326 over 8 years ago - 3 comments

#46 - One logger per module

Issue - State: closed - Opened by julia326 over 8 years ago

#45 - fixes isovar by using new PyEnsembl.Transcript.is_protein_coding property

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

#44 - Error due to PyEnsembl biotypes

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

#42 - Fixed offset computation for mutant residues in protein sequence

Pull Request - State: closed - Opened by iskandr over 8 years ago - 1 comment

#41 - Renamed sub-package 'args' to 'cli' for consistency

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

#40 - Got rid of isovar's variant args parser, using Varcode instead

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

#39 - Fixing name collision of 'gene' DataFrame column

Pull Request - State: closed - Opened by iskandr over 8 years ago - 4 comments

#36 - Update description of algorithm in README

Issue - State: closed - Opened by iskandr over 8 years ago
Labels: docs

#35 - Change scripts into entry_points

Issue - State: closed - Opened by iskandr over 8 years ago - 3 comments
Labels: refactor

#33 - Make sure all commandline arguments match function parameters

Issue - State: open - Opened by iskandr over 8 years ago
Labels: refactor

#32 - Unit tests to ensure that Python & CLI give same results

Issue - State: closed - Opened by iskandr over 8 years ago - 1 comment
Labels: test

#29 - Drop scikit-bio to avoid pinning an old version

Issue - State: closed - Opened by tavinathanson over 8 years ago - 1 comment
Labels: refactor

#26 - Weighted RNA support score for variant sequences

Issue - State: open - Opened by iskandr over 8 years ago - 1 comment
Labels: enhancement

#24 - Add unit test for variant(s) at a splice boundary

Issue - State: open - Opened by iskandr over 8 years ago
Labels: test

#23 - Add unit test for variant read count with indels

Issue - State: open - Opened by iskandr over 8 years ago
Labels: test

#22 - Add ability to skip soft-clipped bases

Issue - State: open - Opened by arahuja over 8 years ago
Labels: enhancement

#21 - Check alt sequence before returning VariantRead

Pull Request - State: closed - Opened by iskandr over 8 years ago - 11 comments

#19 - Wrong cDNA sequence after variant for negative strand transcripts (also affecting counts)

Issue - State: closed - Opened by iskandr almost 9 years ago - 10 comments
Labels: bug

#9 - Pull into Topiary

Issue - State: open - Opened by ihodes almost 9 years ago
Labels: refactor

#8 - Take into account base quality

Issue - State: open - Opened by ihodes almost 9 years ago
Labels: enhancement

#4 - Test data: get co-occurring germline + somatic variants

Issue - State: closed - Opened by iskandr about 9 years ago - 1 comment
Labels: test