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

#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

#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

#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

#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

#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