[extract] Fix crashes when link size exceeds MaxLinkDist

base.go

@@ -102,6 +102,14 @@ var Backend = logging.NewLogBackend(os.Stderr, "", 0)
 // BackendFormatter contains the fancy debug formatter
 var BackendFormatter = logging.NewBackendFormatter(Backend, format)
 
+// ErrorAbort logs an error message and then exit with retcode of 1
+func ErrorAbort(err error) {
+	if err != nil {
+		log.Errorf("%s", err)
+		os.Exit(1)
+	}
+}
+
 // RemoveExt returns the substring minus the extension
 func RemoveExt(filename string) string {
 	return strings.TrimSuffix(filename, path.Ext(filename))

extract.go

@@ -159,7 +159,8 @@ func (r *Extracter) makeModel(outfile string) {
 
 // writeRE write a RE file and report statistics
 func writeRE(outfile string, contigs []*ContigInfo) {
-	f, _ := os.Create(outfile)
+	f, err := os.Create(outfile)
+	ErrorAbort(err)
 	w := bufio.NewWriter(f)
 	defer f.Close()
 	totalCounts := 0

model.go

@@ -113,12 +113,15 @@ func (r *LinkDensityModel) countBinDensities(contigs []*ContigInfo) {
 	// Find the length of assayable intra-contig sequence in each bin
 	intraContigLinkRange := math.Log2(float64(maxLinkDist) / float64(MinLinkDist))
 	nIntraContigBins := int(math.Ceil(intraContigLinkRange * 16))
+	if nIntraContigBins > len(r.nLinks) {
+		nIntraContigBins = len(r.nLinks)
+	}
 
 	// Step 3: loop through all links and tabulate the counts
 	for _, contig := range contigs {
 		for _, link := range contig.links {
 			bin := r.linkBin(link)
-			if bin == -1 {
+			if bin == -1 || bin >= len(r.nLinks) {
 				continue
 			}
 			r.nLinks[bin]++