Merge pull request #7 from bcgsc/release/v1.1.2

Release/v1.1.2

.github/workflows/npm-test.yml

@@ -5,20 +5,25 @@ on: [push]
 jobs:
   build:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        node: [10, 12, 14]
+    name: node-${{ matrix.node }}
     steps:
       - uses: actions/checkout@v2
       - uses: actions/setup-node@v1
         with:
-          node-version: 12
+          node-version: ${{ matrix.node }}
       - run: npm ci
       - run: npm test
       - name: Publish Unit Test Results
         uses: EnricoMi/[email protected]
-        if: always()
+        if: matrix.node == 12
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           files: coverage/junit.xml
       - uses: codecov/codecov-action@v1
         with:
           yml: codecov.yml
           token: ${{ secrets.CODECOV_TOKEN }}
+        if: matrix.node == 12

README.md

@@ -1,6 +1,8 @@
 # GraphKB Parser
 
-[![codecov](https://codecov.io/gh/bcgsc/pori_graphkb_parser/branch/master/graph/badge.svg?token=D3IG5YL6JT)](https://codecov.io/gh/bcgsc/pori_graphkb_parser) ![build](https://github.com/bcgsc/pori_graphkb_parser/workflows/build/badge.svg?branch=master) [![npm version](https://badge.fury.io/js/%40bcgsc-pori%2Fgraphkb-parser.svg)](https://badge.fury.io/js/%40bcgsc-pori%2Fgraphkb-parser)
+[![codecov](https://codecov.io/gh/bcgsc/pori_graphkb_parser/branch/master/graph/badge.svg?token=D3IG5YL6JT)](https://codecov.io/gh/bcgsc/pori_graphkb_parser) ![build](https://github.com/bcgsc/pori_graphkb_parser/workflows/build/badge.svg?branch=master) [![npm version](https://badge.fury.io/js/%40bcgsc-pori%2Fgraphkb-parser.svg)](https://badge.fury.io/js/%40bcgsc-pori%2Fgraphkb-parser) ![node versions](https://img.shields.io/badge/node-10%20%7C%2012%20%7C%2014-blue)
+
+This repository is part of the [platform for oncogenomic reporting and interpretation](https://github.com/bcgsc/pori).
 
 - [About](#about)
 - [Getting Started](#getting-started)
@@ -12,7 +14,7 @@ parsed notation.
 
 ## Getting Started
 
-Import the package
+Import the package (Or try it out online with [RunKit](https://runkit.com/creisle/6083062ff39ff0001b93ea6f))
 
 ```js
 const kbp = require('@bcgsc-pori/graphkb-parser');

codecov.yml

@@ -0,0 +1,6 @@
+coverage:
+  status:
+    project:
+      default:
+        target: 90%
+        threshold: 1%

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bcgsc-pori/graphkb-parser",
-  "version": "1.1.1",
+  "version": "1.1.2",
   "description": "A package for parsing and recreating HGVS-like variant notation used in GraphKB",
   "main": "./src/index.js",
   "directories": {

src/index.js

@@ -4,5 +4,5 @@ const error = require('./error');
 const constants = require('./constants');
 
 module.exports = {
-    variant, position, error, constants,
+    variant, position, error, constants, parse: variant.parse,
 };

src/position.js

@@ -5,7 +5,7 @@ const { ParsingError, InputValidationError } = require('./error');
 const { AA_PATTERN, AA_CODES } = require('./constants');
 
 
-const CDS_PATT = /(\d+)?([-+]\d+)?/;
+const CDS_PATT = /(-?\d+)?([-+]\d+)?/;
 const PROTEIN_PATT = new RegExp(`(${AA_PATTERN})?(\\d+|\\?)`);
 const CYTOBAND_PATT = /[pq]((\d+|\?)(\.(\d+|\?))?)?/;
 
@@ -145,16 +145,22 @@ class IntronicPosition extends BasicPosition {
 }
 
 
-class CdsPosition extends BasicPosition {
+class CdsPosition extends Position {
     /**
      * @param {Object} opt options
      * @param {string} opt.prefix the position prefix
      * @param {Number} opt.offset the offset from the nearest cds position
      */
     constructor(opt) {
-        const { offset } = opt;
+        const { offset, pos } = opt;
         super(opt);
 
+        if (pos === '?' || pos === null) {
+            this.pos = null;
+        } else {
+            this.pos = Number(pos);
+        }
+
         if (offset === null) {
             this.offset = null;
         } else if (offset !== undefined) {
@@ -169,6 +175,7 @@ class CdsPosition extends BasicPosition {
         }
     }
 
+
     toString() {
         let offset = '';
 
@@ -180,7 +187,7 @@ class CdsPosition extends BasicPosition {
             }
             offset = `${offset}${this.offset}`;
         }
-        return `${super.toString(this)}${offset}`;
+        return `${this.pos || '?'}${offset}`;
     }
 
     static get prefix() {

test/variant/continuous.test.js

@@ -260,6 +260,22 @@ describe('coding sequence like', () => {
         expect(result.toString()).toBe(notation);
     });
 
+    test('five prime UTR intron', () => {
+        const notation = 'FEATURE:c.-23+1A>G';
+        const result = parse(notation);
+        const exp = {
+            type: 'substitution',
+            break1Start: { '@class': 'CdsPosition', pos: -23, offset: 1 },
+            break1Repr: 'c.-23+1',
+            reference1: 'FEATURE',
+            refSeq: 'A',
+            untemplatedSeqSize: 1,
+            untemplatedSeq: 'G',
+        };
+        expect(result.toJSON()).toEqual(exp);
+        expect(result.toString()).toBe(notation);
+    });
+
     test('noncoding deletion single bp', () => {
         const notation = 'FEATURE:n.3+1del';
         const result = parse(notation);
@@ -458,15 +474,15 @@ describe('coding sequence like', () => {
         const result = parse(notation);
         const exp = {
             type: NOTATION_TO_TYPES['>'],
-            break1Start: { '@class': 'CdsPosition', pos: 1, offset: -124 },
-            break1Repr: 'c.1-124',
+            break1Start: { '@class': 'CdsPosition', pos: -124, offset: 0 },
+            break1Repr: 'c.-124',
             untemplatedSeq: 'T',
             untemplatedSeqSize: 1,
             refSeq: 'C',
             reference1: 'FEATURE',
         };
         expect(result.toJSON()).toEqual(exp);
-        expect(result.toString()).toBe('FEATURE:c.1-124C>T');
+        expect(result.toString()).toBe('FEATURE:c.-124C>T');
     });
 });