Merge pull request #137 from lifeomic/sequence-id

Added sequence id to create-genomic-set
lifeomic · Mar 5, 2020 · e869544 · e869544
2 parents 7c0fd13 + 67e8999
commit e869544
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Showing 3 changed files with 16 additions and 204 deletions.
diff --git a/lib/cmds/genomics_cmds/create-genomic-set.js b/lib/cmds/genomics_cmds/create-genomic-set.js
@@ -65,6 +65,9 @@ exports.builder = yargs => {
   }).option('test-id', {
     describe: 'The ID of the test to use for grouping related genomic sets.',
     type: 'string'
+  }).option('sequence-id', {
+    describe: 'The ID to use for the FHIR Sequence resource.',
+    type: 'string'
   });
 };
 
@@ -83,7 +86,8 @@ exports.handler = async argv => {
     outputVcfName: argv.outputVcfName,
     passFilter: argv.passFilter,
     updateSample: argv.updateSample,
-    testId: argv.testId
+    testId: argv.testId,
+    sequenceId: argv.sequenceId
   });
   print(response.data, argv);
 };
diff --git a/test/unit/commands/ga4gh-genomicset.test.js b/test/unit/commands/ga4gh-genomicset.test.js
@@ -45,7 +45,8 @@ test.serial.cb('The "ga4gh-genomicsets-create" should create a genomic set', t =
       outputVcfName: 'foo.vcf.gz',
       passFilter: false,
       updateSample: false,
-      testId: undefined
+      testId: undefined,
+      sequenceId: undefined
     });
     t.is(printSpy.callCount, 1);
     t.is(printSpy.getCall(0).args[0], res.data);