From 7ebf9a90a0309d4627bfa537872273dba5087c25 Mon Sep 17 00:00:00 2001
From: Fengchao <fcyucn@gmail.com>
Date: Tue, 6 Feb 2024 10:27:39 -0500
Subject: [PATCH] Remove a redundant "best position" column.

---
 lib/id/pep.go     | 2 --
 lib/rep/psm.go    | 4 +---
 lib/spc/pepxml.go | 1 -
 3 files changed, 1 insertion(+), 6 deletions(-)

diff --git a/lib/id/pep.go b/lib/id/pep.go
index 6ce78f22..3030ef40 100644
--- a/lib/id/pep.go
+++ b/lib/id/pep.go
@@ -117,7 +117,6 @@ type MSFraggerLoc struct {
 	IonsSecondBestPosition   string
 	IonsAllUnshifted         string
 	IonsShiftedAllPositioins string
-	BestPosition             string
 }
 
 // PepIDList is a list of PeptideSpectrumMatch
@@ -511,7 +510,6 @@ func processSpectrumQuery(sq spc.SpectrumQuery, mods mod.Modifications, decoyTag
 				IonsSecondBestPosition:   i.PTMResult.IonsSecondBestPosition,
 				IonsAllUnshifted:         i.PTMResult.IonsAllUnshifted,
 				IonsShiftedAllPositioins: i.PTMResult.IonsShiftedAllPositions,
-				BestPosition:             i.PTMResult.BestPosition,
 			}
 		}
 
diff --git a/lib/rep/psm.go b/lib/rep/psm.go
index fb7e9d13..ebda5fb0 100644
--- a/lib/rep/psm.go
+++ b/lib/rep/psm.go
@@ -238,7 +238,6 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 	if hasLoc {
 		header += "\tMSFragger Localization" +
 			"\tPosition Scores" +
-			"\tBest Position" +
 			"\tScore Best Position" +
 			"\tIons Best Position" +
 			"\tScore Second Best Position" +
@@ -630,11 +629,10 @@ 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\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",
 				line,
 				MSFraggerLoc.LocalizationPeptide,
 				MSFraggerLoc.PositionScores,
-				MSFraggerLoc.BestPosition,
 				MSFraggerLoc.ScoreBestPosition,
 				MSFraggerLoc.IonsBestPosition,
 				MSFraggerLoc.ScoreSecondBestPosition,
diff --git a/lib/spc/pepxml.go b/lib/spc/pepxml.go
index 5662d329..6c3184c1 100644
--- a/lib/spc/pepxml.go
+++ b/lib/spc/pepxml.go
@@ -228,5 +228,4 @@ 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"`
-	BestPosition             string `xml:"best_position,attr"`
 }