Merge pull request #134 from Nesvilab/dev

Dev

Changelog

@@ -7,4 +7,5 @@
 - The number of tryptic ternmini is now determined by ProteinProphet.
 
 ### Fixed
-- Error preventing iTRAQ quantification.
+- Error preventing iTRAQ quantification.
+- Several formatting, typoes and Go-Vet issues were fixed.

README.md

@@ -3,7 +3,8 @@
 </p>
 
 [![Release](https://img.shields.io/github/release/nesvilab/philosopher.svg?color=purple&style=for-the-badge)](https://github.com/Nesvilab/philosopher/releases/latest)
-![Golang](https://img.shields.io/badge/Go-1.13.1-blue.svg?style=for-the-badge)
+![Golang](https://img.shields.io/badge/Go-1.14.2-blue.svg?style=for-the-badge)
+[![Go Report Card](https://goreportcard.com/badge/github.com/Nesvilab/philosopher?style=for-the-badge&color=red&logo=appveyor)](https://goreportcard.com/report/github.com/Nesvilab/philosopher)
 ![GitHub](https://img.shields.io/github/license/Nesvilab/philosopher?style=for-the-badge)
 ![](https://img.shields.io/github/downloads/Nesvilab/philosopher/total.svg?color=red&style=for-the-badge)
 ![GitHub Workflow Status](https://img.shields.io/github/workflow/status/Nesvilab/philosopher/philosopher-build?style=for-the-badge)
@@ -36,7 +37,6 @@
 - Multi-level detailed reports for peptides, ions, and proteins.
 
 
-
 ## Download
 Download the latest version [here](https://github.com/nesvilab/philosopher/releases/latest).
 
@@ -70,7 +70,6 @@ Still in progress!
 [Alexey Nesvizhskii's research group](http://www.nesvilab.org/)
 
 
-
 ## Questions, requests and bug reports
 If you have any questions, remarks, requests or if you found a bug, please use the [Issue tracker](https://github.com/nesvilab/philosopher/issues).
 

cmd/abacus.go

@@ -9,6 +9,7 @@ import (
 	"philosopher/lib/met"
 	"philosopher/lib/msg"
 	"philosopher/lib/sys"
+
 	"github.com/spf13/cobra"
 )
 

cmd/bioquant.go

@@ -8,6 +8,7 @@ import (
 	"philosopher/lib/msg"
 	"philosopher/lib/qua"
 	"philosopher/lib/sys"
+
 	"github.com/spf13/cobra"
 )
 
@@ -24,7 +25,7 @@ var bioquantCmd = &cobra.Command{
 		// run clustering
 		qua.RunBioQuantification(m)
 
-		// store paramters on meta data
+		// store parameters on meta data
 		m.Serialize()
 
 		// clean tmp

cmd/comet.go

@@ -8,6 +8,7 @@ import (
 	"philosopher/lib/met"
 	"philosopher/lib/msg"
 	"philosopher/lib/sys"
+
 	"github.com/spf13/cobra"
 )
 

cmd/database.go

@@ -22,7 +22,7 @@ var databaseCmd = &cobra.Command{
 
 		m = dat.Run(m)
 
-		// store paramters on meta data
+		// store parameters on meta data
 		m.Serialize()
 
 		msg.Done()

cmd/freequant.go

@@ -10,6 +10,7 @@ import (
 	"philosopher/lib/msg"
 	"philosopher/lib/qua"
 	"philosopher/lib/sys"
+
 	"github.com/spf13/cobra"
 )
 
@@ -43,7 +44,7 @@ var freequant = &cobra.Command{
 		// run label-free quantification
 		qua.RunLabelFreeQuantification(m.Quantify)
 
-		// store paramters on meta data
+		// store parameters on meta data
 		m.Serialize()
 
 		// clean tmp

cmd/inspect.go

@@ -6,11 +6,12 @@ import (
 	"os"
 	"path/filepath"
 
-	"github.com/davecgh/go-spew/spew"
 	"philosopher/lib/dat"
 	"philosopher/lib/met"
 	"philosopher/lib/msg"
 	"philosopher/lib/rep"
+
+	"github.com/davecgh/go-spew/spew"
 	"github.com/spf13/cobra"
 	"github.com/vmihailenco/msgpack"
 )

cmd/iproph.go

@@ -8,6 +8,7 @@ import (
 	"philosopher/lib/met"
 	"philosopher/lib/msg"
 	"philosopher/lib/sys"
+
 	"github.com/spf13/cobra"
 )
 

cmd/labelquant.go

@@ -47,7 +47,7 @@ var labelquantCmd = &cobra.Command{
 
 		m.Quantify = qua.RunIsobaricLabelQuantification(m.Quantify, m.Filter.Mapmods)
 
-		// store paramters on meta data
+		// store parameters on meta data
 		m.Serialize()
 
 		// clean tmp

cmd/proproph.go

@@ -8,6 +8,7 @@ import (
 	"philosopher/lib/met"
 	"philosopher/lib/msg"
 	"philosopher/lib/sys"
+
 	"github.com/spf13/cobra"
 )
 
@@ -49,7 +50,7 @@ func init() {
 		proprophCmd.Flags().BoolVarP(&m.ProteinProphet.Fpkm, "fpkm", "", false, "model protein FPKM values")
 		proprophCmd.Flags().BoolVarP(&m.ProteinProphet.NonSP, "nonsp", "", false, "do not use NSP model")
 		proprophCmd.Flags().IntVarP(&m.ProteinProphet.Minindep, "minindep", "", 0, "minimum percentage of independent peptides required for a protein")
-		proprophCmd.Flags().Float64VarP(&m.ProteinProphet.Minprob, "minprob", "", 0.05, "PeptideProphet probabilty threshold")
+		proprophCmd.Flags().Float64VarP(&m.ProteinProphet.Minprob, "minprob", "", 0.05, "PeptideProphet probability threshold")
 		proprophCmd.Flags().IntVarP(&m.ProteinProphet.Maxppmdiff, "maxppmdiff", "", 2000000, "maximum peptide mass difference in ppm")
 		proprophCmd.Flags().BoolVarP(&m.ProteinProphet.Accuracy, "accuracy", "", false, "equivalent to --minprob 0")
 		proprophCmd.Flags().BoolVarP(&m.ProteinProphet.Normprotlen, "normprotlen", "", false, "normalize NSP using protein length")

cmd/report.go

@@ -8,6 +8,7 @@ import (
 	"philosopher/lib/msg"
 	"philosopher/lib/rep"
 	"philosopher/lib/sys"
+
 	"github.com/spf13/cobra"
 )
 

cmd/root.go

@@ -4,12 +4,13 @@ package cmd
 import (
 	"runtime"
 
-	colorable "github.com/mattn/go-colorable"
-	"github.com/sirupsen/logrus"
-	"github.com/spf13/cobra"
 	"philosopher/lib/met"
 	"philosopher/lib/msg"
 	"philosopher/lib/sys"
+
+	colorable "github.com/mattn/go-colorable"
+	"github.com/sirupsen/logrus"
+	"github.com/spf13/cobra"
 )
 
 var m met.Data
@@ -24,7 +25,7 @@ var (
 // RootCmd represents the base command when called without any subcommands
 var RootCmd = &cobra.Command{
 	Use:   "philosopher",
-	Short: "philospher: a proteomics data analysis toolkit",
+	Short: "philosopher: a proteomics data analysis toolkit",
 	Long:  "Philosopher: A toolkit for Proteomics data analysis and post-processing filtering",
 }
 

cmd/tmtintegrator.go

@@ -8,6 +8,7 @@ import (
 	"philosopher/lib/met"
 	"philosopher/lib/msg"
 	"philosopher/lib/sys"
+
 	"github.com/spf13/cobra"
 )
 

cmd/version.go

@@ -5,6 +5,7 @@ import (
 	"os"
 
 	"philosopher/lib/gth"
+
 	"github.com/sirupsen/logrus"
 	"github.com/spf13/cobra"
 )

cmd/workspace.go

@@ -5,9 +5,10 @@ import (
 	"fmt"
 	"os"
 
-	ga "github.com/jpillora/go-ogle-analytics"
 	"philosopher/lib/msg"
 	"philosopher/lib/wrk"
+
+	ga "github.com/jpillora/go-ogle-analytics"
 	"github.com/spf13/cobra"
 )
 

go.sum

@@ -2,6 +2,8 @@
 4d63.com/gochecknoglobals v0.0.0-20190306162314-7c3491d2b6ec/go.mod h1:Sk40JNJmh0koZukOjJfaBNLZazbZthFfHnLHIcZNS6A=
 cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw=
 dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU=
+github.com/AndreasBriese/bbloom v0.0.0-20190306092124-e2d15f34fcf9 h1:HD8gA2tkByhMAwYaFAX9w2l7vxvBQ5NMoxDrkhqhtn4=
+github.com/AndreasBriese/bbloom v0.0.0-20190306092124-e2d15f34fcf9/go.mod h1:bOvUY6CB00SOBii9/FifXqc0awNKxLFCL/+pkDPuyl8=
 github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU=
 github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym/WlBOVXweHU+Q+/VP0lqqI8lqeDx9IjBqo=
 github.com/OneOfOne/xxhash v1.2.2/go.mod h1:HSdplMjZKSmBqAxg5vPj2TmRDmfkzw+cTzAElWljhcU=
@@ -17,8 +19,10 @@ github.com/alexkohler/nakedret v1.0.0 h1:S/bzOFhZHYUJp6qPmdXdFHS5nlWGFmLmoc8QOyd
 github.com/alexkohler/nakedret v1.0.0/go.mod h1:tfDQbtPt67HhBK/6P0yNktIX7peCxfOp0jO9007DrLE=
 github.com/armon/consul-api v0.0.0-20180202201655-eb2c6b5be1b6/go.mod h1:grANhF5doyWs3UAsr3K4I6qtAmlQcZDesFNEHPZAzj8=
 github.com/beorn7/perks v0.0.0-20180321164747-3a771d992973/go.mod h1:Dwedo/Wpr24TaqPxmxbtue+5NUziq4I4S80YR8gNf3Q=
+github.com/beorn7/perks v1.0.0 h1:HWo1m869IqiPhD389kmkxeTalrjNbbJTC8LXupb+sl0=
 github.com/beorn7/perks v1.0.0/go.mod h1:KWe93zE9D1o94FZ5RNwFwVgaQK1VOXiVxmqh+CedLV8=
 github.com/boombuler/barcode v1.0.0/go.mod h1:paBWMcWSl3LHKBqUq+rly7CNSldXjb2rDl3JlRe0mD8=
+github.com/cespare/xxhash v1.1.0 h1:a6HrQnmkObjyL+Gs60czilIUGqrzKutQD6XZog3p+ko=
 github.com/cespare/xxhash v1.1.0/go.mod h1:XrSqR1VqqWfGrhpAt58auRo0WTKS1nRRg3ghfAqPWnc=
 github.com/client9/misspell v0.3.4/go.mod h1:qj6jICC3Q7zFZvVWo7KLAzC3yx5G7kyvSDkc90ppPyw=
 github.com/coreos/bbolt v1.3.2/go.mod h1:iRUV2dpdMOn7Bo10OQBFzIJO9kkE559Wcmn+qkEiiKk=
@@ -33,8 +37,15 @@ github.com/creack/pty v1.1.9/go.mod h1:oKZEueFk5CKHvIhNR5MUki03XCEU+Q6VDXinZuGJ3
 github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
+github.com/dgraph-io/badger v1.6.1 h1:w9pSFNSdq/JPM1N12Fz/F/bzo993Is1W+Q7HjPzi7yg=
+github.com/dgraph-io/badger v1.6.1/go.mod h1:FRmFw3uxvcpa8zG3Rxs0th+hCLIuaQg8HlNV5bjgnuU=
+github.com/dgraph-io/ristretto v0.0.2 h1:a5WaUrDa0qm0YrAAS1tUykT5El3kt62KNZZeMxQn3po=
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+github.com/dgryski/go-farm v0.0.0-20190423205320-6a90982ecee2/go.mod h1:SqUrOPUnsFjfmXRMNPybcSiG0BgUW2AuFH8PAnS2iTw=
 github.com/dgryski/go-sip13 v0.0.0-20181026042036-e10d5fee7954/go.mod h1:vAd38F8PWV+bWy6jNmig1y/TA+kYO4g3RSRF0IAv0no=
+github.com/dustin/go-humanize v1.0.0 h1:VSnTsYCnlFHaM2/igO1h6X3HA71jcobQuxemgkq4zYo=
+github.com/dustin/go-humanize v1.0.0/go.mod h1:HtrtbFcZ19U5GC7JDqmcUSB87Iq5E25KnS6fMYU6eOk=
 github.com/fogleman/gg v1.2.1-0.20190220221249-0403632d5b90 h1:WXb3TSNmHp2vHoCroCIB1foO/yQ36swABL8aOVeDpgg=
 github.com/fogleman/gg v1.2.1-0.20190220221249-0403632d5b90/go.mod h1:R/bRT+9gY/C5z7JzPU0zXsXHKM4/ayA+zqcVNZzPa1k=
 github.com/fogleman/gg v1.3.0 h1:/7zJX8F6AaYQc57WQCyN9cAIz+4bCJGO9B+dyW29am8=
@@ -49,6 +60,8 @@ github.com/go-logfmt/logfmt v0.4.0/go.mod h1:3RMwSq7FuexP4Kalkev3ejPJsZTpXXBr9+V
 github.com/go-stack/stack v1.8.0/go.mod h1:v0f6uXyyMGvRgIKkXu+yp6POWl0qKG85gN/melR3HDY=
 github.com/gogo/protobuf v1.1.1/go.mod h1:r8qH/GZQm5c6nD/R0oafs1akxWv10x8SbQlK7atdtwQ=
 github.com/gogo/protobuf v1.2.1/go.mod h1:hp+jE20tsWTFYpLwKvXlhS1hjn+gTNwPg2I6zVXpSg4=
+github.com/gojp/goreportcard v0.0.0-20200415071653-59167b516f3f h1:9ZmDy86ZrqIHVGK/ZA0/gRogDx9ZHBc3U8+yX5DpQA4=
+github.com/gojp/goreportcard v0.0.0-20200415071653-59167b516f3f/go.mod h1:/DA2Xpp+OaR3EHafQSnT9SKOfbG2NPQR/qp6Qr8AgIw=
 github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0 h1:DACJavvAHhabrF08vX0COfcOBJRhZ8lUbR+ZWIs0Y5g=
 github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0/go.mod h1:E/TSTwGwJL78qG/PmXZO1EjYhfJinVAhrmmHX6Z8B9k=
 github.com/golang/glog v0.0.0-20160126235308-23def4e6c14b/go.mod h1:SBH7ygxi8pfUlaOkMMuAQtPIUF8ecWP5IEl/CR7VP2Q=
@@ -122,6 +135,7 @@ github.com/mattn/go-isatty v0.0.10 h1:qxFzApOv4WsAL965uUPIsXzAKCZxN2p9UqdhFS4ZW1
 github.com/mattn/go-isatty v0.0.10/go.mod h1:qgIWMr58cqv1PHHyhnkY9lrL7etaEgOFcMEpPG5Rm84=
 github.com/mattn/go-isatty v0.0.12 h1:wuysRhFDzyxgEmMf5xjvJ2M9dZoWAXNNr5LSBS7uHXY=
 github.com/mattn/go-isatty v0.0.12/go.mod h1:cbi8OIDigv2wuxKPP5vlRcQ1OAZbq2CE4Kysco4FUpU=
+github.com/matttproud/golang_protobuf_extensions v1.0.1 h1:4hp9jkHxhMHkqkrB3Ix0jegS5sx/RkqARlsWZ6pIwiU=
 github.com/matttproud/golang_protobuf_extensions v1.0.1/go.mod h1:D8He9yQNgCq6Z5Ld7szi9bcBfOoFv/3dc6xSMkL2PC0=
 github.com/mdempsky/unconvert v0.0.0-20190921185256-3ecd357795af h1:teodtdq5zEa8oY1giGuheGJCzSzbMA0wCpnbZ0jEcGc=
 github.com/mdempsky/unconvert v0.0.0-20190921185256-3ecd357795af/go.mod h1:9+3Wp2ccIz73BJqVfc7n2+1A+mzvnEwtDTqEjeRngBQ=
@@ -156,12 +170,16 @@ github.com/pkg/errors v0.9.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINE
 github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=
 github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
 github.com/prometheus/client_golang v0.9.1/go.mod h1:7SWBe2y4D6OKWSNQJUaRYU/AaXPKyh/dDVn+NZz0KFw=
+github.com/prometheus/client_golang v0.9.3 h1:9iH4JKXLzFbOAdtqv/a+j8aewx2Y8lAjAydhbaScPF8=
 github.com/prometheus/client_golang v0.9.3/go.mod h1:/TN21ttK/J9q6uSwhBd54HahCDft0ttaMvbicHlPoso=
 github.com/prometheus/client_model v0.0.0-20180712105110-5c3871d89910/go.mod h1:MbSGuTsp3dbXC40dX6PRTWyKYBIrTGTE9sqQNg2J8bo=
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+github.com/prometheus/common v0.4.0 h1:7etb9YClo3a6HjLzfl6rIQaU+FDfi0VSX39io3aQ+DM=
 github.com/prometheus/common v0.4.0/go.mod h1:TNfzLD0ON7rHzMJeJkieUDPYmFC7Snx/y86RQel1bk4=
 github.com/prometheus/procfs v0.0.0-20181005140218-185b4288413d/go.mod h1:c3At6R/oaqEKCNdg8wHV1ftS6bRYblBhIjjI8uT2IGk=
+github.com/prometheus/procfs v0.0.0-20190507164030-5867b95ac084 h1:sofwID9zm4tzrgykg80hfFph1mryUeLRsUfoocVVmRY=
 github.com/prometheus/procfs v0.0.0-20190507164030-5867b95ac084/go.mod h1:TjEm7ze935MbeOT/UhFTIMYKhuLP4wbCsTZCD3I8kEA=
 github.com/prometheus/tsdb v0.7.1/go.mod h1:qhTCs0VvXwvX/y3TZrWD7rabWM+ijKTux40TwIPHuXU=
 github.com/prvst/philosopher v1.5.1 h1:w9qhIRm17Im4FwOq1+5TQsY6zfwOAcyh5XbwmRZzFaY=
@@ -181,6 +199,7 @@ github.com/sirupsen/logrus v1.4.2 h1:SPIRibHv4MatM3XXNO2BJeFLZwZ2LvZgfQ5+UNI2im4
 github.com/sirupsen/logrus v1.4.2/go.mod h1:tLMulIdttU9McNUspp0xgXVQah82FyeX6MwdIuYE2rE=
 github.com/soheilhy/cmux v0.1.4/go.mod h1:IM3LyeVVIOuxMH7sFAkER9+bJ4dT7Ms6E4xg4kGIyLM=
 github.com/spaolacci/murmur3 v0.0.0-20180118202830-f09979ecbc72/go.mod h1:JwIasOWyU6f++ZhiEuf87xNszmSA2myDM2Kzu9HwQUA=
+github.com/spaolacci/murmur3 v1.1.0/go.mod h1:JwIasOWyU6f++ZhiEuf87xNszmSA2myDM2Kzu9HwQUA=
 github.com/spf13/afero v1.1.2/go.mod h1:j4pytiNVoe2o6bmDsKpLACNPDBIoEAkihy7loJ1B0CQ=
 github.com/spf13/cast v1.3.0/go.mod h1:Qx5cxh0v+4UWYiBimWS+eyWzqEqokIECu5etghLkUJE=
 github.com/spf13/cobra v0.0.5 h1:f0B+LkLX6DtmRH1isoNA9VTtNUK9K8xYd28JNNfOv/s=
@@ -198,6 +217,7 @@ github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+
 github.com/stretchr/objx v0.1.1/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
 github.com/stretchr/testify v1.2.2 h1:bSDNvY7ZPG5RlJ8otE/7V6gMiyenm9RtJ7IUVIAoJ1w=
 github.com/stretchr/testify v1.2.2/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs=
+github.com/stretchr/testify v1.4.0/go.mod h1:j7eGeouHqKxXV5pUuKE4zz7dFj8WfuZ+81PSLYec5m4=
 github.com/stretchr/testify v1.5.1 h1:nOGnQDM7FYENwehXlg/kFVnos3rEvtKTjRvOWSzb6H4=
 github.com/stretchr/testify v1.5.1/go.mod h1:5W2xD1RspED5o8YsWQXVCued0rvSQ+mT+I5cxcmMvtA=
 github.com/tmc/grpc-websocket-proxy v0.0.0-20190109142713-0ad062ec5ee5/go.mod h1:ncp9v5uamzpCO7NfCPTXjqaC+bZgJeR0sMTm6dMHP7U=
@@ -275,6 +295,7 @@ golang.org/x/sys v0.0.0-20190312061237-fead79001313/go.mod h1:h1NjWce9XRLGQEsW7w
 golang.org/x/sys v0.0.0-20190412213103-97732733099d/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
 golang.org/x/sys v0.0.0-20190422165155-953cdadca894 h1:Cz4ceDQGXuKRnVBDTS23GTn/pU5OE2C0WrNTOYK1Uuc=
 golang.org/x/sys v0.0.0-20190422165155-953cdadca894/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/sys v0.0.0-20190626221950-04f50cda93cb/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
 golang.org/x/sys v0.0.0-20191001151750-bb3f8db39f24/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
 golang.org/x/sys v0.0.0-20191008105621-543471e840be/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
 golang.org/x/sys v0.0.0-20191115151921-52ab43148777 h1:wejkGHRTr38uaKRqECZlsCsJ1/TGxIyFbH32x5zUdu4=
@@ -300,6 +321,7 @@ golang.org/x/tools v0.0.0-20190311212946-11955173bddd/go.mod h1:LCzVGOaR6xXOjkQ3
 golang.org/x/tools v0.0.0-20190312151545-0bb0c0a6e846/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs=
 golang.org/x/tools v0.0.0-20190325161752-5a8dccf5b48a h1:iEgSlyueP+hVXFS7PZk7z5e23iHin+tpXArziYTt574=
 golang.org/x/tools v0.0.0-20190325161752-5a8dccf5b48a/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs=
+golang.org/x/tools v0.0.0-20200207183749-b753a1ba74fa h1:5E4dL8+NgFOgjwbTKz+OOEGGhP+ectTmF842l6KjupQ=
 golang.org/x/tools v0.0.0-20200207183749-b753a1ba74fa/go.mod h1:TB2adYChydJhpapKDTa4BR/hXlZSLoq2Wpct/0txZ28=
 golang.org/x/xerrors v0.0.0-20191011141410-1b5146add898/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
 gonum.org/v1/gonum v0.0.0-20180816165407-929014505bf4 h1:nYxTaCPaVoJbxx+vMVnsFb6kw5+6aJCx52m/lmM/Vog=

lib/bio/bio_test.go

@@ -110,7 +110,6 @@ func TestAminoAcids(t *testing.T) {
 		t.Errorf("Aminoacid name is incorrect, got %s, want %s", a.Name, "Valine")
 	}
 
-	tes.ShutDowTestEnv()
 }
 
 // func TestProtonMass(t *testing.T) {
@@ -145,6 +144,4 @@ func TestEnzymes(t *testing.T) {
 	if e.Name != "glu_c" {
 		t.Errorf("Enzyme is incorrect, got %s, want %s", e.Name, "glu_c")
 	}
-
-	tes.ShutDowTestEnv()
 }

lib/cla/cla.go

@@ -13,7 +13,8 @@ import (
 func IsDecoyPSM(p id.PeptideIdentification, tag string) bool {
 
 	// default for TRUE (DECOY)
-	var class = true
+	// updated to FALSE
+	var class bool
 
 	if strings.HasPrefix(p.Protein, tag) {
 		class = true
@@ -38,8 +39,9 @@ func IsDecoyPSM(p id.PeptideIdentification, tag string) bool {
 // IsDecoyProtein identifies a Protein as target or Decoy based on the decoy tag
 func IsDecoyProtein(p id.ProteinIdentification, tag string) bool {
 
-	// default for TRUE ( DECOY)
-	var class = true
+	// default for TRUE (DECOY)
+	// updated to FALSE
+	var class bool
 
 	if strings.HasPrefix(string(p.ProteinName), tag) {
 		class = true
@@ -53,8 +55,9 @@ func IsDecoyProtein(p id.ProteinIdentification, tag string) bool {
 // IsDecoy identifies a Protein as target or Decoy based on the decoy tag
 func IsDecoy(name string, tag string) bool {
 
-	// default for TRUE ( DECOY)
-	var class = true
+	// default for TRUE (DECOY)
+	// updated to FALSE
+	var class bool
 
 	if strings.HasPrefix(name, tag) {
 		class = true

lib/dat/dat.go

@@ -249,10 +249,14 @@ func (d *Base) Deploy(temp string) {
 
 	d.CrapDB = fmt.Sprintf("%s%scrap.fas", temp, string(filepath.Separator))
 
-	param, e := Asset("crap.fas")
-	e = ioutil.WriteFile(d.CrapDB, param, sys.FilePermission())
-	if e != nil {
-		msg.WriteFile(e, "fatal")
+	param, e1 := Asset("crap.fas")
+	if e1 != nil {
+		msg.WriteFile(e1, "fatal")
+	}
+
+	e2 := ioutil.WriteFile(d.CrapDB, param, sys.FilePermission())
+	if e2 != nil {
+		msg.WriteFile(e2, "fatal")
 	}
 
 	return
@@ -314,7 +318,7 @@ func (d *Base) Save(home, temp, tag string, isRev, hasIso, noD, Crap bool) strin
 	return outfile
 }
 
-// Serialize saves to disk a msgpack verison of the database data structure
+// Serialize saves to disk a msgpack version of the database data structure
 func (d *Base) Serialize() {
 
 	b, e := msgpack.Marshal(&d)