fixing ineff. assig.

lib/ext/comet/win/win.go

@@ -24,30 +24,33 @@ func WinParameterFile(winParam string) {
 	return
 }
 
-// Win32 deploys win32 bits comt parameter file
+// Win32 deploys win32 bits comet parameter file
 func Win32(win32 string) {
 
 	bin, e := Asset("comet.2019011.win32.exe")
 	if e != nil {
-		msg.DeployAsset(errors.New("Comet Windows binary file"), "fatal")
+		msg.DeployAsset(errors.New("Comet Windows binary file"), "Cannot read Comet bin")
 	}
 
 	e = ioutil.WriteFile(win32, bin, sys.FilePermission())
 	if e != nil {
-		msg.DeployAsset(errors.New("Comet Windows binary file"), "fatal")
+		msg.DeployAsset(errors.New("Comet Windows binary file"), "Cannot deploy Comet")
 	}
 
 	return
 }
 
-// Win64 deploys win64 bits comt parameter file
+// Win64 deploys win64 bits comet parameter file
 func Win64(win64 string) {
 
 	bin, e := Asset("comet.2019011.win64.exe")
-	e = ioutil.WriteFile(win64, bin, sys.FilePermission())
+	if e != nil {
+		msg.DeployAsset(errors.New("Comet Windows binary file"), "Cannot read Comet bin")
+	}
 
+	e = ioutil.WriteFile(win64, bin, sys.FilePermission())
 	if e != nil {
-		msg.DeployAsset(errors.New("Comet Windows binary file"), "fatal")
+		msg.DeployAsset(errors.New("Comet Windows binary file"), "Cannot deploy Comet")
 	}
 
 	return

lib/fin/fin.go

@@ -1241,7 +1241,7 @@ func binaryread(r io.Reader, data interface{}) {
 // data, and returns the position in the file afterwards
 func readAt(rs io.ReadSeeker, pos uint64, v Version, data reader) uint64 {
 
-	spos, e1 := rs.Seek(int64(pos), 0)
+	_, e1 := rs.Seek(int64(pos), 0)
 	if e1 != nil {
 		msg.Custom(errors.New("error seeking file"), "fatal")
 	}

lib/id/pep.go

@@ -647,7 +647,8 @@ func printModel(v, path string, xAxis, obs, pos, neg []float64) {
 func tdclassifier(p PeptideIdentification, tag string) bool {
 
 	// default for TRUE ( DECOY)
-	var class = true
+	//var class = true
+	var class bool
 
 	if strings.HasPrefix(string(p.Protein), tag) {
 		class = true

lib/qua/qua.go

@@ -102,7 +102,7 @@ func RunIsobaricLabelQuantification(p met.Quantify, mods bool) met.Quantify {
 
 		mappedPurity := calculateIonPurity(p.Dir, p.Format, mz, sourceMap[sourceList[i]])
 
-		var labels = make(map[string]iso.Labels)
+		var labels map[string]iso.Labels
 		if p.Level == 3 {
 			labels = prepareLabelStructureWithMS3(p.Dir, p.Format, p.Brand, p.Plex, p.Tol, mz)
 
@@ -122,7 +122,7 @@ func RunIsobaricLabelQuantification(p met.Quantify, mods bool) met.Quantify {
 				psmMap[j.Spectrum] = psm
 			}
 		}
-		mappedPurity = nil
+		//mappedPurity = nil
 
 		for _, j := range mappedPSM {
 			v, ok := psmMap[j.Spectrum]
@@ -132,7 +132,7 @@ func RunIsobaricLabelQuantification(p met.Quantify, mods bool) met.Quantify {
 				psmMap[j.Spectrum] = psm
 			}
 		}
-		mappedPSM = nil
+		//mappedPSM = nil
 
 	}
 
@@ -143,7 +143,7 @@ func RunIsobaricLabelQuantification(p met.Quantify, mods bool) met.Quantify {
 			evi.PSM[i].Labels = v.Labels
 		}
 	}
-	psmMap = nil
+	//psmMap = nil
 
 	// classification and filtering based on quality filters
 	logrus.Info("Filtering spectra for label quantification")
@@ -186,7 +186,7 @@ func RunIsobaricLabelQuantification(p met.Quantify, mods bool) met.Quantify {
 func RunBioQuantification(c met.Data) {
 
 	// create clean reference db for clustering
-	clusterFasta := createCleanDataBaseReference(c.UUID, c.Temp)
+	//clusterFasta := createCleanDataBaseReference(c.UUID, c.Temp)
 
 	// run cdhit, create cluster file
 	logrus.Info("Clustering")