From 0c25dc3219a0abf2dd433d2ebae2e5b622350e90 Mon Sep 17 00:00:00 2001
From: Mark Schroering <mark.schroering@lifeomic.com>
Date: Thu, 14 Nov 2019 15:02:11 -0500
Subject: [PATCH] Add option to update sample name when creating a genomic set

---
 lib/cmds/genomics_cmds/create-genomic-set.js | 7 ++++++-
 test/unit/commands/ga4gh-genomicset.test.js  | 3 ++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/lib/cmds/genomics_cmds/create-genomic-set.js b/lib/cmds/genomics_cmds/create-genomic-set.js
index 318bf99..fc46b5c 100644
--- a/lib/cmds/genomics_cmds/create-genomic-set.js
+++ b/lib/cmds/genomics_cmds/create-genomic-set.js
@@ -58,6 +58,10 @@ exports.builder = yargs => {
     describe: 'Update the filter for all variants to be PASS',
     type: 'boolean',
     default: false
+  }).option('update-sample', {
+    describe: 'Update the VCF sample name to a unique value',
+    type: 'boolean',
+    default: false
   });
 };
 
@@ -74,7 +78,8 @@ exports.handler = async argv => {
     indexedDate: argv.indexedDate,
     performerId: argv.performerId,
     outputVcfName: argv.outputVcfName,
-    passFilter: argv.passFilter
+    passFilter: argv.passFilter,
+    updateSample: argv.updateSample
   });
   print(response.data, argv);
 };
diff --git a/test/unit/commands/ga4gh-genomicset.test.js b/test/unit/commands/ga4gh-genomicset.test.js
index c1bbba7..b4e0ff3 100644
--- a/test/unit/commands/ga4gh-genomicset.test.js
+++ b/test/unit/commands/ga4gh-genomicset.test.js
@@ -43,7 +43,8 @@ test.serial.cb('The "ga4gh-genomicsets-create" should create a genomic set', t =
       performerId: 'performer1',
       indexedDate: '1999-01-01 12:00',
       outputVcfName: 'foo.vcf.gz',
-      passFilter: false
+      passFilter: false,
+      updateSample: false
     });
     t.is(printSpy.callCount, 1);
     t.is(printSpy.getCall(0).args[0], res.data);