Propagate two shifted-ion-only-related scores to psm.tsv

Author: fcyu

Diff for: lib/id/pep.go

@@ -117,6 +117,8 @@ type MSFraggerLoc struct {
 	IonsSecondBestPosition   string
 	IonsAllUnshifted         string
 	IonsShiftedAllPositioins string
+	ShiftedOnlyScores        string
+	ShiftedOnlyIons          string
 }
 
 // PepIDList is a list of PeptideSpectrumMatch
@@ -510,6 +512,8 @@ func processSpectrumQuery(sq spc.SpectrumQuery, mods mod.Modifications, decoyTag
 				IonsSecondBestPosition:   i.PTMResult.IonsSecondBestPosition,
 				IonsAllUnshifted:         i.PTMResult.IonsAllUnshifted,
 				IonsShiftedAllPositioins: i.PTMResult.IonsShiftedAllPositions,
+				ShiftedOnlyScores:        i.PTMResult.ShiftedOnlyScores,
+				ShiftedOnlyIons:          i.PTMResult.ShiftedOnlyIons,
 			}
 		}
 

Diff for: lib/rep/psm.go

@@ -238,6 +238,8 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 	if hasLoc {
 		header += "\tMSFragger Localization" +
 			"\tPosition Scores" +
+			"\tShifted Only Position Scores" +
+			"\tShifted Only Position Ions" +
 			"\tScore Best Position" +
 			"\tIons Best Position" +
 			"\tScore Second Best Position" +
@@ -629,10 +631,12 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 			if MSFraggerLoc == nil {
 				MSFraggerLoc = &id.MSFraggerLoc{}
 			}
-			line = fmt.Sprintf("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s",
+			line = fmt.Sprintf("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s",
 				line,
 				MSFraggerLoc.LocalizationPeptide,
 				MSFraggerLoc.PositionScores,
+				MSFraggerLoc.ShiftedOnlyScores,
+				MSFraggerLoc.ShiftedOnlyIons,
 				MSFraggerLoc.ScoreBestPosition,
 				MSFraggerLoc.IonsBestPosition,
 				MSFraggerLoc.ScoreSecondBestPosition,

Diff for: lib/spc/pepxml.go

@@ -228,4 +228,6 @@ type PTMResult struct {
 	IonsShiftedAllPositions  string `xml:"ions_shifted_all_positions,attr"`
 	ScoreShiftedBestPosition string `xml:"score_shifted_best_position,attr"`
 	IonsShiftedBestPosition  string `xml:"ions_shifted_best_position,attr"`
+	ShiftedOnlyScores        string `xml:"shifted_only_position_scores,attr"`
+	ShiftedOnlyIons          string `xml:"shifted_only_position_ions,attr"`
 }