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Branch: master
Commits on Jan 30, 2019
  1. Added check for missing header to schema validation in python API.

    javh committed Jan 30, 2019
Commits on Dec 5, 2018
  1. R tests (#167)

    ssnn-airr authored and javh committed Dec 5, 2018
    Updated R package test data and associated unit tests to use 1-based coordinates.
Commits on Oct 15, 2018
  1. Fix error in MiAIRR-to-NCBI doc

    bussec committed Oct 1, 2018
  2. Fix typo

    bussec committed Oct 1, 2018
  3. Update SRA libary_* mapping

    bussec committed May 16, 2018
  4. Update IgBLAST version for AIRR v1.2 schema support in docs.

    javh committed Oct 15, 2018
Commits on Oct 5, 2018
  1. Python library bug fix - v1.2.1 (#160)

    javh committed Oct 5, 2018
    * Fixed a bug with start coordinate conversion leading to empty values in python library writer class.
    * Updated python library NEWS.
Commits on Sep 28, 2018
  1. Changed contact email (#159)

    williamdlees authored and javh committed Sep 28, 2018
    Changed software working group contact email in docs.
Commits on Sep 13, 2018
  1. Schema terminology updates. (#153)

    javh committed Sep 13, 2018
    Schema description updates with consistent use of "gene" and "segment".
Commits on Sep 10, 2018
  1. several fixes for actual CEDAR and template ops

    graybeal authored and schristley committed Sep 2, 2018
Commits on Sep 1, 2018
  1. Sw tools initial (#151)

    williamdlees committed Sep 1, 2018
    * First commit of software tools standard
    
    * Minor corrections
    
    * Grammar/Layout tidy-up
    
    * Add contact emails for completed questionnaires
    
    * Proofread and organization changes.
    
    * Typo.
    
    * Changed email contact for submissions to
    tools-standard@airr-community.org
Commits on Aug 28, 2018
  1. Minor correction ot DataRep example docs.

    javh committed Aug 28, 2018
  2. add command to run unit tests

    schristley committed Aug 21, 2018
  3. add info slot

    schristley committed Aug 21, 2018
  4. add doc

    schristley committed Aug 21, 2018
  5. copy schema to R

    schristley committed Aug 21, 2018
  6. add info to schema

    schristley committed Aug 21, 2018
  7. info object

    schristley committed Aug 20, 2018
Commits on Aug 17, 2018
  1. Update Rearrangement support table in docs to v1.2 schema.

    javh committed Aug 17, 2018
  2. Switched `toy_data.tsv` start positions to 1-based.

    javh committed Aug 17, 2018
  3. Another typo...

    javh committed Aug 17, 2018
  4. Long travis build.

    javh committed Aug 17, 2018
  5. Typo.

    javh committed Aug 17, 2018
  6. Rearrangement doc polish.

    javh committed Aug 17, 2018
  7. Poke Travis.

    javh committed Aug 17, 2018
Commits on Aug 16, 2018
  1. Minor changes to docs toc tree.

    javh committed Aug 16, 2018
  2. Rearrangement updates for v1.2 (#149)

    javh committed Aug 16, 2018
    Various updates for v1.2
    
    * Swap to 1-based coordinates and fill optional columns with explicit optional label in docs.
    * Set default coordinate scheme to "1" in R package.
    * Python package Windows fix
    * Removal of automatic handle closure upon end of RearrangementReader iteration.
    * Added `Encoding` field to R package DESCRIPTION file.
    * Rewrite python validation and update tests
    * Added doc text about custom columns in the Rearrangement TSV.
    * Corrected some doc terminology and adding a table of software supporting the Rearrangement spec.
    * Sync terminology between manuscript and docs.
    * Fixed terminology in R package and updated news.
    * Added `base` argument to the Rearrangement reader/writer in the python library to control conversion of 0-based and 1-based coordinates.
    * Added dataset definition to docs.
    * Moved validate methods in python library to schema objects. Some performance tweaks.
    * Swapped python `airr.interface` functions to accept file paths instead of handles and changed `airr.interface.validate_rearrangement` to process only a single file.
    * Modified bad_data2.tsv to have of one each kind of bad value and no missing fields. Added bad_data3.tsv with missing fields and bad values.
    * Fixed R travis build
    * Add germline_alignment data to R rearrangement example file.
    * Simplified R example TSV sequence_id values.
    * Bumped R package version and rebuilt R docs.
    * Fixed formatting of downloadable tables for Rearrangement and Alignment field definitions.
    * Updated package NEWS.