fixed bug with id-specific charge states being merged incorrectly; up…

…dated readme

FlashLFQ/FlashLfqEngine.cs

@@ -1053,7 +1053,7 @@ private List<FlashLFQFeature> MainFileSearch(string fileName, Dictionary<double,
                 return concurrentBagOfFeatures.ToList();
 
             var identifications = identificationsForThisFile.ToList();
-
+            
             Parallel.ForEach(Partitioner.Create(0, identifications.Count),
                 new ParallelOptions { MaxDegreeOfParallelism = maxThreads },
                 (range, loopState) =>
@@ -1259,7 +1259,7 @@ private void RunErrorChecking(List<FlashLFQFeature> features)
                             {
                                 if (feature.intensity != -1)
                                 {
-                                    var featuresToMerge = group.Where(p => Math.Abs(p.apexPeak.peakWithScan.retentionTime - feature.apexPeak.peakWithScan.retentionTime) < rtTol && p.intensity != -1);
+                                    var featuresToMerge = group3.Where(p => Math.Abs(p.apexPeak.peakWithScan.retentionTime - feature.apexPeak.peakWithScan.retentionTime) < rtTol && p.intensity != -1);
                                     if (featuresToMerge.Any())
                                         feature.MergeFeatureWith(featuresToMerge, integrate);
                                 }

README.md

@@ -1,3 +1,50 @@
-# FlashLFQ
+# About
+FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. 
 
-FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.
+# Requirements
+Input is a tab-separated value (TSV) text file of MS/MS identifications, in addition to one or more raw data files. Currently, .mzml and .raw files are supported. ThermoMSFileReader v3.10 is required to read .raw files. A 64-bit machine running Microsoft Windows is also required.
+
+# Download
+To download the latest standalone version of FlashLFQ, go [here](https://github.com/smith-chem-wisc/FlashLFQ/releases/latest). Click the .zip file (e.g. FlashLFQ.v0.1.*.zip) and extract the contents to a desired location on your computer. 
+
+FlashLFQ is bundled into MetaMorpheus, which can be downloaded [here](https://github.com/smith-chem-wisc/MetaMorpheus). MetaMorpheus is a full-featured GUI proteomics software suite that features mass-calibration, PTM-discovery, search algorithms, and FlashLFQ label-free quantification built in.
+
+# Usage
+FlashLFQ is currently a command-line program, though it is also built into the MetaMorpheus GUI (see [MetaMorpheus](https://github.com/smith-chem-wisc/MetaMorpheus)).
+
+To use the FlashLFQ standalone version, run the "FlashLFQExecutable" program with command-line arguments.
+
+
+**Accepted arguments:**
+
+*--idt [string|identification file path (TSV format)]*
+*--raw [string|MS data file (.raw or .mzml)]*
+*--rep [string|directory containing MS data files]*
+*--ppm [double|ppm tolerance] (default = 10)*
+*--iso [double|isotopic distribution tolerance in ppm] (default = 5)*
+*--sil [bool|silent mode] (default = false)*
+*--pau [bool|pause at end of run] (default = true)*
+*--int [bool|integrate features] (default = false)*
+*--chg [bool|use only precursor charge state] (default = false)*
+
+**Examples:**
+
+*FlashLFQExecutable --idt "C:\MyFolder\msms.txt" --rep "C:\MyFolder" --ppm 5*
+
+*FlashLFQExecutable --idt "C:\MyFolder\msms.txt" --raw "C:\MyFolder\MyRawFile.raw" --ppm 5 --iso 3 --sil true --pau false --int true --chg false*
+
+# Output
+FlashLFQ outputs several text files, described here:
+*Log.txt*
+*QuantifiedPeaks.tsv*
+*QuantifiedBaseSequences.tsv*
+*QuantifiedModifiedSequences.tsv*
+
+The .tsv files are convenient to view with Microsoft Excel.
+
+# Development Status
+To do: 
+- Retention time calibration/matching between runs (currently in an early state)
+- Improved peak picking
+- Intensity normalization (especially between technical replicates, biological replicates, and fractions)
+- Protein quantification