Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / griffithlab/pVAC-Seq issues and pull requests
#338 - Improvements to Wildtype plugin
Pull Request -
State: closed - Opened by willmclaren almost 7 years ago
- 2 comments
#334 - Die if the wildtype amino acid in the wildtype sequence is different from the one in the amino acid change
Pull Request -
State: closed - Opened by susannasiebert about 7 years ago
- 1 comment
#332 - Fix bug with handling certain frameshift variants
Pull Request -
State: closed - Opened by susannasiebert about 7 years ago
- 1 comment
#324 - Input Parsing for Vaccine Design
Pull Request -
State: closed - Opened by mnneveau about 7 years ago
- 3 comments
#319 - Paging, filtering, and sorting methods
Pull Request -
State: closed - Opened by amberzw about 7 years ago
#315 - Vaccine Visualization
Pull Request -
State: closed - Opened by mnneveau about 7 years ago
- 9 comments
#309 - Add new endpoints & update tests and swagger
Pull Request -
State: closed - Opened by amberzw over 7 years ago
#307 - Remove unnecessary line of code
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
#302 - fix formatting typo
Pull Request -
State: closed - Opened by ryanking over 7 years ago
- 1 comment
#300 - Vaccine design
Pull Request -
State: closed - Opened by jneich over 7 years ago
#298 - Version compatibility
Pull Request -
State: open - Opened by agraubert over 7 years ago
#297 - Add new parameter user_tool to iedb calls to leverage queueing capabilities
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
- 2 comments
#295 - Added vaccine design script and unit test
Pull Request -
State: closed - Opened by jneich over 7 years ago
- 14 comments
#294 - Add option to append sample name as a new column to the report
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
- 1 comment
#292 - Write yml log file of inputs used
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
- 2 comments
#291 - Handle MNPs at beginning of full sequence
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
#289 - Use total number of matching AAs instead of number of consecutive matching AAs
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
#288 - Add functionality to be able to handle DNPs when generating the fasta
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
- 2 comments
#279 - respone_text from IEDB is byte not str - handle accordingly
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
#276 - Fix typo in header
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
#275 - Strip additional lines from IEDB output
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
#274 - Wait 60 seconds between requests to the IEDB API
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
- 8 comments
#273 - use max epitope length instead of min for cutoff
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
#272 - Don't open filehandles by command to avoid too many open filehandles error
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
- 1 comment
#266 - Fix bug for sequences that have no cleavage positions
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
#265 - Improve the way we sort our result files
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
#264 - Fix IEDB Class II bug
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
#262 - Check that there is a score for a method before trying to use it
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
#253 - Remove unneeded check for valid alleles and replace with a warning.
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
- 1 comment
#252 - Update IEDB RESTful-API URL
Pull Request -
State: closed - Opened by susannasiebert over 7 years ago
- 1 comment
#250 - New class for variants
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
- 1 comment
#243 - Attempt to handle mysterious str comparison error
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
- 1 comment
#242 - Integrate fusion processing into the pipeline
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
#241 - Fix a bug in the main pvacseq test that would skip diffing some output files
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
- 1 comment
#240 - Some more types of frameshifts that we need to skip
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
#238 - Handle variants that are start lost
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
- 1 comment
#237 - Only check the sample genotype if the VCF contains a sample
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
#235 - Add subclasses for fusion processing
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
- 3 comments
#233 - Check run return code from local IEDB install before proceeding
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
- 1 comment
#229 - Centralize "Split" File Path Generation
Pull Request -
State: open - Opened by tmooney almost 8 years ago
- 2 comments
#228 - Fix an error when the last row in the input tsv happens to fall on the end of an even chunk.
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
#226 - Handle repetitive inframe indel at beginning of the sequence
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
#224 - New command to output a fasta for vaccine design
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
- 4 comments
#218 - Skip variants that are hom_ref or uncalled
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
#217 - Create the additional_input_file_list.yaml in code
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
#215 - Support a local install path for IEDB
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
- 1 comment
#214 - Update test execution in test_pvacseq.py
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
#213 - Replace print and flush with a status_message subroutine
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
#212 - Add a new column for the mutation position in the sub-peptide
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
- 3 comments
#211 - Only try to close the filehandle if it has been created previously
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
- 3 comments
#210 - Hotfix release - v4.0.1
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
#209 - Fix compatibility issues with new IEDB version
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
#208 - Check all keys in nested dict before accessing element
Pull Request -
State: closed - Opened by susannasiebert almost 8 years ago
- 3 comments
#205 - Add a iedb_retries parameter to controll how many calls to IEDB are made
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#204 - Merge hotfix branch into master
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
#203 - Don't reprocess TSV if it already exists
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#202 - Subset the list of all alleles to class I and class II before processing further
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 3 comments
#200 - Make certain scripts into classes in preparation for fusion addition
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
#199 - Fix syntax error in setup.py
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 1 comment
#198 - Remove pvacseq.egg-info folder from git tree
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#197 - Really merge flask branch into develop (and not master)
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
#196 - Merge flask branch into develop
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
#189 - Update incorrect usage information
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
Labels: bug
#188 - Merge develop into master for 4.0.0 release
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
#187 - Sphinx documentation files for ReadTheDocs
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
#186 - Use the top_score_metric to also pick the appropriate fold change column for filtering
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 3 comments
#185 - Add column with all NetChop cleavage scores
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 4 comments
#183 - Rename and reorder report columns
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 3 comments
#182 - Rename class_i and class_ii dirs to MHC_Class_I and MHC_Class_II
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#181 - Use 'NA' instead of leaving certain columns blank
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 4 comments
#180 - Handle case where no additional_input_file_list is provided
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#179 - Handle fasta sequences that contain * to prevent downstream errors
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#178 - Remove certain subcommands for individual steps
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 3 comments
#175 - Add a downstream-sequence-length parameter to limit the length of frameshift downstream sequences in the fasta
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#174 - Add bam-readcount output as additional input files to pvacseq
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#173 - When chunking the fasta use the actual number of entries in the file
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#171 - Filter fasta sequences to prevent downstream errors
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#165 - Reworked package_data to allow development installs
Pull Request -
State: closed - Opened by agraubert about 8 years ago
- 1 comment
#164 - Use a yaml file to list additional input files instead of individual params
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 4 comments
#163 - New version 3.0.5
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
#160 - Add MHC Class II predictions
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#159 - Increase csv.field_size_limit
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#157 - Handle edge case for inframe deletion positional range.
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
Labels: bug
#156 - Added allele field to NetMHCstab output
Pull Request -
State: closed - Opened by agraubert about 8 years ago
- 2 comments
#152 - Rename output files for clarity
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#151 - Handle empty FPKM fields
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#150 - Rename output files for clarity
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 3 comments
#149 - Reorder subcommands and arguments
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#148 - Fix a bug preventing more than 9 sequences per chunk in netmhcstab
Pull Request -
State: closed - Opened by agraubert about 8 years ago
- 1 comment
#147 - Add pipeline class in preparation for adding class II predictions
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#146 - Make a class to replace pvacseq_utils in preparation for adding Class II predictions
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#144 - Added NetMHCStab to pipeline
Pull Request -
State: closed - Opened by agraubert about 8 years ago
- 2 comments
#142 - Only create tmp directory if it doesn't exist yet
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#141 - Add option to provide Cufflinks files for FPKM filtering
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 12 comments
#140 - Hotfix release - v3.0.4
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
#139 - Write files to a temporary location before copying into final location
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 3 comments
#135 - Don't run parse and combine if there are no input files
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#131 - Write intermediate files to a tmp directory under main output directory
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 4 comments
#130 - Add new option to specify fasta chunk size
Pull Request -
State: closed - Opened by susannasiebert about 8 years ago
- 2 comments
#125 - Added Net chop to pipeline
Pull Request -
State: closed - Opened by agraubert about 8 years ago
- 6 comments