Update README.md

README.md

@@ -1,5 +1,4 @@
-# SLMTransform
-SLM-Transform: Fast and Memory-Efficient MS/MS Spectra Indexing for Peptide Search in Mass-Spectrometry based Proteomics
+# CFIR Index
 
 ## Authors
 Muhammad Haseeb and Fahad Saeed
@@ -9,69 +8,52 @@ Muhammad Haseeb and Fahad Saeed
 2. GCC v5.4.0 or later with C++11+ support
 2. Windows: MinGW (x86_64-6.3.0-win32-seh-rt_v5-rev2)
 
-# Pre SLM-Transform Steps
+# Pre CFIR-Index Steps
 1. Digest the proteome database using Protein Digestion Simulator or OpenMS.
 2. Remove the redundant peptide sequences in the digested database using DBToolkit.
 3. Optional: The decoy database can be generated and appended to the target database using DBToolkit.
 4. Convert the MS/MS data in (mzML/MS2) format using msconvert.exe. The MS/MS data are extracted and processed by MSToolkit.
 
 # The Sample Driver Application
-The sample application shows the software pipeline for successfully incorporating SLM-Transform for peptide search. The application firsts initializes SLM Peptide and Ions Index (SPI and SII) respectively. Then the raw fragment-ion match score based query is conducted against SLM-Index. The driver application creates an array called Matches (99999 hits x 1000 queries) which is filled with index number of candidate PSMs using SLM-Querying algorithm. The candidate PSMs can be further processed or filtered as required by the application. However, the sample application just discards the results and records the execution time only. There is another version of sample application; that counts the PSMs discovered per query peptide. That application can be used to measure stats and can be requested from authors by email if required. 
+The sample application shows the software pipeline for successfully incorporating CFIR-Index for peptide search. The application firsts initializes Peptide and Ions Index respectively. Then the raw fragment-ion match score based query is conducted against CFIR-Index. The driver application creates an array called Matches (99999 hits x 1000 queries) which is filled with index number of candidate PSMs using CFIR-Querying algorithm. The candidate PSMs can be further processed or filtered as required by the application. However, the sample application just discards the results and records the execution time only. There is another version of sample application; that counts the PSMs discovered per query peptide. That application can be used to measure stats and can be requested from authors by email if required. 
 
-# Configure SLM-Transform & Sample Application
-1. Configure the SLM-Transform parameters in /slmtransform/include/config.h: 
+# Configure CFIR-Index & Sample Application
+1. Configure the CFIR-Index parameters in /slmtransform/include/config.h: 
 *Make sure that #define/undef WINDOWS is correct according to your Host OS else there will be Seg faults.*
-2. Add the database, dataset and mods information in the ./slm.cpp (Sample Application) using the following format:
+2. Add the mods information in the ./slm.cpp (Sample Application) using the following format:
 
 ## Format
-
-    STRING modconditions = "#1 <res> #2"; 
-    /* #1 is maximum allowed modified residues per sequence, 
-    <res> modified residues of 1st type, 
-    #2 how many residues of this modification in peptide sequence. 
-
-    For example: we want max 5 mod residues; and max STY 3 and max M 2 we will set modconditions as
-    "5 STY 3 M 2"
-    */
-
-    <some code> 
-
-    /* Database and Dataset files */
-    STRING filename = "/path/to/digested/and/unduplicated/database.fasta"; // Path to processed database
-    STRING querypath = "/path/to/query/dataset"; // Path to Dataset folder
-    STRING patt = ".ms2/mzML/mzXML"; // Keep one, remove others
-
     <some code> 
 
     /* Initialize the vModInfo */
-    vModInfo.num_vars = #3; // Types of modifications been specified (max 7) for above example, set this to: 2
-    vModInfo.vmods_per_pep = #1; // #1 from the previous explanation, from above example, set this to: 5
+    vModInfo.num_vars = #; // Types of modifications been specified (max 7)
+    vModInfo.vmods_per_pep = #; // Number of modified AAs per peptide
 
     /* List of Mods Info */
-    vModInfo.vmods[0].aa_per_peptide = 3// #2 from previous explanation, for above example, set this to: 3
-    vModInfo.vmods[0].modMass = 79.97 * SCALE; // Mass of the specified modification, for above example: 79.97
-    vModInfo.vmods[0].residues[0] = 'S'; // modified residues list (max 4 per mod type allowed), for above example S
+    vModInfo.vmods[0].aa_per_peptide = #; // Number of modified AAs of this modification type
+    vModInfo.vmods[0].modMass = # * SCALE; // Mass of the specified modification, for example: 79.97
+    vModInfo.vmods[0].residues[0] = 'S'; // modified residues list (max 4 per mod type allowed), for example S
     vModInfo.vmods[0].residues[1] = 'T'; // T
     vModInfo.vmods[0].residues[2] = 'Y'; // Y
 
-    vModInfo.vmods[0].aa_per_peptide = 2; // #2 from previous explanation, for above example, set this to: 2
-    vModInfo.vmods[0].modMass = 15.997 * SCALE; // Mass of the specified modification, for above example: 15.997
-    vModInfo.vmods[0].residues[0] = 'M'; // modified residues list (max 4 per mod type allowed), for above example M
+    vModInfo.vmods[0].aa_per_peptide = #; // Number of modified AAs of this modification type
+    vModInfo.vmods[0].modMass = 15.997 * SCALE; // Mass of the specified modification, for example: 15.997
+    vModInfo.vmods[0].residues[0] = 'M'; // modified residues list (max 4 per mod type allowed), for example M
 
-# Building SLM-Transform Sample Application
+# Building CFIR-Index Sample Application
 1. Open the Git Bash shell (Windows) or normal Terminal (Ubuntu).
-1. Navigate to SLM-Transform home directory /slmtransform/
+1. Navigate to CFIR-Index home directory /cfir/
 2. Execute the following command: `make`
 
-# Running SLM-Transform Sample Application
-1. Navigate to /slmtransform
+# Running CFIR-Index Sample Application
+1. Navigate to /cfir
 2. ./SLMTransform.exe
 
 # Please Note:
-1. Work is being done to move SLM-Transform configuration to runtime so please bear with us.
+1. We are integrating a full file based parameter parser for configuration settings to runtime.
 2. Max digested peptide mass allowed: 5000Da.
-3. The SLM-Transform only returns the fragment-ion filtered PSMs (not the final PSMs), which can be used in any way e.g. post filtered based on precursor masses or sequence tags, formally scored for PSMs, FDRed.
+3. The CFIR-Index only returns the shared-peak count scores not the XCorr scores, which can be used in any way e.g. post filtered based on precursor masses or sequence tags, formally scored for PSMs, FDRed.
 4. Please contact us if you experience any trouble or bugs in the software. Thanks. :)
 
 # Please cite our work
-For queries or questions about SLM-Transform, please contact: {fsaeed, mhaseeb}@fiu.edu. Thank you.
+For queries or questions about CFIR-Index, please contact: {fsaeed, mhaseeb}@fiu.edu. Thank you.