From 15cbf603dda3b9773c1cdd0c5b03cf1046e9eff0 Mon Sep 17 00:00:00 2001
From: Brent Pedersen <bpederse@gmail.com>
Date: Fri, 5 May 2017 13:12:21 -0600
Subject: [PATCH] use single-threaded bgzf until I figure out race

---
 api/api.go      | 19 ++-----------------
 docs/CHANGES.md |  4 ++++
 vcfanno.go      |  2 +-
 3 files changed, 7 insertions(+), 18 deletions(-)

diff --git a/api/api.go b/api/api.go
index e2f15c5..b9952ac 100644
--- a/api/api.go
+++ b/api/api.go
@@ -5,7 +5,6 @@ import (
 	"log"
 	"os"
 	"reflect"
-	"runtime"
 	"strconv"
 	"strings"
 	"sync"
@@ -661,16 +660,8 @@ func (a *Annotator) Setup(query HeaderUpdater) ([]interfaces.Queryable, error) {
 	}
 	var wg sync.WaitGroup
 	wg.Add(len(files))
-	workers := 1
-	if runtime.GOMAXPROCS(0) > len(files) && len(files) > 0 {
-		workers = imax(2, runtime.GOMAXPROCS(0)/len(files))
-		if workers > 3 {
-			workers = 3
-		}
-		log.Printf("vcfanno: using ~%d workers per file", workers)
-	}
-
 	queryables := make([]interfaces.Queryable, len(files))
+	workers := 1
 	for i, file := range files {
 		go func(idx int, file string) {
 			var q interfaces.Queryable
@@ -678,13 +669,7 @@ func (a *Annotator) Setup(query HeaderUpdater) ([]interfaces.Queryable, error) {
 			if strings.HasSuffix(file, ".bam") {
 				q, err = parsers.NewBamQueryable(file, 2)
 			} else {
-				if getSize(file) > 2320303098 {
-					q, err = bix.New(file, workers+1)
-				} else if getSize(file) < 120303098 {
-					q, err = bix.New(file, 1)
-				} else {
-					q, err = bix.New(file, workers)
-				}
+				q, err = bix.New(file, workers)
 			}
 			if err != nil {
 				log.Fatal(err)
diff --git a/docs/CHANGES.md b/docs/CHANGES.md
index 4369b65..abc410a 100644
--- a/docs/CHANGES.md
+++ b/docs/CHANGES.md
@@ -1,3 +1,7 @@
+v0.2.6
+------
++ fix race condition from 0.2.4 by reverting some speed improvements from that release.
+
 v0.2.5
 ------
 + better error messages
diff --git a/vcfanno.go b/vcfanno.go
index df9555e..af29a34 100644
--- a/vcfanno.go
+++ b/vcfanno.go
@@ -25,7 +25,7 @@ import (
 	"github.com/brentp/xopen"
 )
 
-var VERSION = "0.2.5"
+var VERSION = "0.2.6"
 
 func envGet(name string, vdefault int) int {
 	sval := os.Getenv(name)