From 2600c707b73c1396f817335167ee2c22b3355378 Mon Sep 17 00:00:00 2001
From: Lei Lu <lonelu@users.noreply.github.com>
Date: Mon, 28 Jun 2021 12:27:23 -0700
Subject: [PATCH] quick fix file loading done (#2064)

* Try to update mzLib 466 to 471

* Add ReadSpectralLibrary_pDeep

* DoneWithFile

* Delete yeast2fake_pdeep_lib.msp

Co-authored-by: Robert Millikin <rmillikin@wisc.edu>
---
 TaskLayer/GlycoSearchTask/GlycoSearchTask.cs | 2 ++
 TaskLayer/XLSearchTask/XLSearchTask.cs       | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/TaskLayer/GlycoSearchTask/GlycoSearchTask.cs b/TaskLayer/GlycoSearchTask/GlycoSearchTask.cs
index cf4ad4996..2dcb8c509 100644
--- a/TaskLayer/GlycoSearchTask/GlycoSearchTask.cs
+++ b/TaskLayer/GlycoSearchTask/GlycoSearchTask.cs
@@ -99,6 +99,8 @@ protected override MyTaskResults RunSpecific(string OutputFolder, List<DbForTask
                 Status("Getting ms2 scans...", thisId);
 
                 Ms2ScanWithSpecificMass[] arrayOfMs2ScansSortedByMass = GetMs2Scans(myMsDataFile, origDataFile, combinedParams).OrderBy(b => b.PrecursorMass).ToArray();
+                myFileManager.DoneWithFile(origDataFile);
+
                 List<GlycoSpectralMatch>[] newCsmsPerMS2ScanPerFile = new List<GlycoSpectralMatch>[arrayOfMs2ScansSortedByMass.Length];
 
                 for (int currentPartition = 0; currentPartition < CommonParameters.TotalPartitions; currentPartition++)
diff --git a/TaskLayer/XLSearchTask/XLSearchTask.cs b/TaskLayer/XLSearchTask/XLSearchTask.cs
index 7418e2ab4..8bdfa14fa 100644
--- a/TaskLayer/XLSearchTask/XLSearchTask.cs
+++ b/TaskLayer/XLSearchTask/XLSearchTask.cs
@@ -95,7 +95,7 @@ protected override MyTaskResults RunSpecific(string OutputFolder, List<DbForTask
                 Status("Getting ms2 scans...", thisId);
 
                 Ms2ScanWithSpecificMass[] arrayOfMs2ScansSortedByMass = GetMs2Scans(myMsDataFile, origDataFile, combinedParams).OrderBy(b => b.PrecursorMass).ToArray();
-
+                myFileManager.DoneWithFile(origDataFile);
                 List<CrosslinkSpectralMatch>[] newCsmsPerMS2ScanPerFile = new List<CrosslinkSpectralMatch>[arrayOfMs2ScansSortedByMass.Length];
                 for (int currentPartition = 0; currentPartition < CommonParameters.TotalPartitions; currentPartition++)
                 {