From e4839e500e2da73b476f095425c0347ae7c5de97 Mon Sep 17 00:00:00 2001
From: Tom Clegg <tom@curii.com>
Date: Mon, 17 Jan 2022 13:03:44 -0500
Subject: [PATCH] Use native client to read annotations.csv.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
---
 anno2vcf.go    | 9 +++++++--
 exportnumpy.go | 2 +-
 vcf2fasta.go   | 2 +-
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/anno2vcf.go b/anno2vcf.go
index 23c6f21ece..85d89eb458 100644
--- a/anno2vcf.go
+++ b/anno2vcf.go
@@ -10,7 +10,6 @@ import (
 	"flag"
 	"fmt"
 	"io"
-	"io/ioutil"
 	"net/http"
 	_ "net/http/pprof"
 	"os"
@@ -118,10 +117,16 @@ func (cmd *anno2vcf) RunCommand(prog string, args []string, stdin io.Reader, std
 		filename := *inputDir + "/" + fi.Name()
 		thr.Go(func() error {
 			log.Printf("reading %s", filename)
-			buf, err := ioutil.ReadFile(filename)
+			f, err := open(filename)
+			if err != nil {
+				return err
+			}
+			defer f.Close()
+			buf, err := io.ReadAll(f)
 			if err != nil {
 				return fmt.Errorf("%s: %s", filename, err)
 			}
+			f.Close()
 			lines := bytes.Split(buf, []byte{'\n'})
 			calls := map[string][]*call{}
 			for lineIdx, line := range lines {
diff --git a/exportnumpy.go b/exportnumpy.go
index c5a2b7af4e..27c86a3210 100644
--- a/exportnumpy.go
+++ b/exportnumpy.go
@@ -411,7 +411,7 @@ func makeMask(regionsFilename string, expandRegions int) (*mask, error) {
 		return nil, err
 	}
 	defer rfile.Close()
-	regions, err := ioutil.ReadAll(rfile)
+	regions, err := io.ReadAll(rfile)
 	if err != nil {
 		return nil, err
 	}
diff --git a/vcf2fasta.go b/vcf2fasta.go
index e1a3a3944e..3ca18c410f 100644
--- a/vcf2fasta.go
+++ b/vcf2fasta.go
@@ -475,7 +475,7 @@ func (cmd *vcf2fasta) loadRegionsPy() error {
 		if resp.StatusCode != http.StatusOK {
 			return fmt.Errorf("get %q: http status %d", cmd.gvcfRegionsPy, resp.StatusCode)
 		}
-		buf, err := ioutil.ReadAll(resp.Body)
+		buf, err := io.ReadAll(resp.Body)
 		if err != nil {
 			return fmt.Errorf("get %q: read body: %s", cmd.gvcfRegionsPy, err)
 		}
-- 
2.30.2