From 766ce66958305cb6e25e48fe5a0937504edf8edb Mon Sep 17 00:00:00 2001
From: Bryson Gibbons <bryson.gibbons@pnnl.gov>
Date: Tue, 9 Oct 2018 16:37:16 -0700
Subject: [PATCH] Bump version and update readme

---
 MzidMerger/MzidMerger.csproj | 2 +-
 readme.md                    | 5 ++++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/MzidMerger/MzidMerger.csproj b/MzidMerger/MzidMerger.csproj
index 812ab9e..1cdf9fd 100644
--- a/MzidMerger/MzidMerger.csproj
+++ b/MzidMerger/MzidMerger.csproj
@@ -6,7 +6,7 @@
     <RootNamespace>MzidMerger</RootNamespace>
     <AssemblyName>MzidMerger</AssemblyName>
     <PackageId>MzidMerger</PackageId>
-    <Version>1.1.0</Version>
+    <Version>1.2.0</Version>
     <AssemblyVersion>$(Version)</AssemblyVersion>
     <FileVersion>$(Version)</FileVersion>
     <Description>Merges mzid[.gz] files into a single mzid[.gz]. Designed for MS-GF+ mzid files (looks for SpecEValue scores)</Description>
diff --git a/readme.md b/readme.md
index 021b813..caab3e6 100644
--- a/readme.md
+++ b/readme.md
@@ -13,7 +13,7 @@ MzidMerger uses PSI_Interface.dll for reading and writing the mzids.
 
 ## Syntax
 
-`MzidMerger -inDir "directory path" [-filter "filename filter"] [-out "output file path"] [-maxSpecEValue number] [-keepOnlyBestResults]`
+`MzidMerger -inDir "directory path" [-filter "filename filter"] [-out "output file path"] [-maxSpecEValue number] [-keepOnlyBestResults] [-fixIds]`
 
 ### Required parameters:
 `-inDir path` 
@@ -32,6 +32,9 @@ MzidMerger uses PSI_Interface.dll for reading and writing the mzids.
 `-keepOnlyBestResults`
 * If specified, only the best-scoring results for each spectrum are kept.
 
+`-fixIds`
+* Fix the peptide and peptideEvidence IDs. Only use for e.g. older MS-GF+ results, that output many errors about duplicate IDs. Only fixes Peptide and PeptideEvidence IDs.
+
 ## Contacts
 
 Written by Bryson Gibbons and Matthew Monroe for the Department of Energy (PNNL, Richland, WA) \