use single-threaded bgzf until I figure out race

brentp · May 5, 2017 · 15cbf60 · 15cbf60
1 parent 9c41f9e
commit 15cbf60
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Showing 3 changed files with 7 additions and 18 deletions.
diff --git a/api/api.go b/api/api.go
@@ -5,7 +5,6 @@ import (
 	"log"
 	"os"
 	"reflect"
-	"runtime"
 	"strconv"
 	"strings"
 	"sync"
@@ -661,30 +660,16 @@ 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
 			var err 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
@@ -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
@@ -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)