@sjcrh/proteinpaint-rust 2.39.0 → 2.44.0

package/Cargo.toml

@@ -19,14 +19,13 @@ plotters = "0.3.4"
 colorgrad = "0.6.2"
 statrs = "^0.16.0"
 fishers_exact="^1.0.1"
-bio = "^0.39"
+bio = "1.5.0"
 bigtools = "^0.1.11"
 libmath = "^0.2.1"
 json = "^0.12.4"
 serde = {version = "^1.0.147", features = ["derive"]}
 serde_json="^1.0.88"
 num = "^0.4.1"
-csv = "^1.2.2"
 r_mathlib="^0.2.0"
 tokio = { version="1", features = ["full"] }
 reqwest = "0.11"

package/package.json

@@ -1,37 +1,37 @@
 {
-  "version": "2.39.0",
-  "name": "@sjcrh/proteinpaint-rust",
-  "description": "Rust-based utilities for proteinpaint",
-  "main": "index.js",
-  "bin": {
-    "proteinpaint-rust": "index.js"
-  },
-  "scripts": {
-    "dev": "cargo build --release",
-    "build": "cargo build --release",
-    "postinstall": "if [ ! -d ./test ] & [ ! -d ./target/release ]; then cargo build --release; fi",
-    "test": "tape **/test/*.spec.js",
-    "test:unit": "tape **/test/*.unit.spec.js",
-    "test:integration": "echo 'TODO: rust integration tests'"
-  },
-  "author": "Robin Paul",
-  "license": "SEE LICENSE IN ./LICENSE",
-  "repository": {
-    "type": "git",
-    "url": "https://github.com/stjude/proteinpaint.git",
-    "directory": "rust"
-  },
-  "files": [
-    "index.js",
-    "Cargo.toml",
-    "src",
-    "LICENSE/*"
-  ],
-  "bugs": {
-    "url": "https://github.com/stjude/proteinpaint"
-  },
-  "homepage": "https://github.com/stjude/proteinpaint#readme",
-  "devDependencies": {
-    "tape": "^5.2.2"
-  }
+	"version": "2.44.0",
+	"name": "@sjcrh/proteinpaint-rust",
+	"description": "Rust-based utilities for proteinpaint",
+	"main": "index.js",
+	"bin": {
+		"proteinpaint-rust": "index.js"
+	},
+	"scripts": {
+		"dev": "cargo clean && cargo build --release",
+		"build": "cargo clean && cargo build --release",
+		"postinstall": "if [ ! -d ./test ] & [ ! -d ./target/release ]; then cargo clean && cargo build --release; fi",
+		"test": "tape **/test/*.spec.js",
+		"test:unit": "tape **/test/*.unit.spec.js",
+		"test:integration": "echo 'TODO: rust integration tests'"
+	},
+	"author": "Robin Paul",
+	"license": "SEE LICENSE IN ./LICENSE",
+	"repository": {
+		"type": "git",
+		"url": "https://github.com/stjude/proteinpaint.git",
+		"directory": "rust"
+	},
+	"files": [
+		"index.js",
+		"Cargo.toml",
+		"src",
+		"LICENSE/*"
+	],
+	"bugs": {
+		"url": "https://github.com/stjude/proteinpaint"
+	},
+	"homepage": "https://github.com/stjude/proteinpaint#readme",
+	"devDependencies": {
+		"tape": "^5.2.2"
+	}
 }

package/src/DEanalysis.rs

@@ -1,5 +1,5 @@
 // cd .. && cargo build --release && json='{"case":"SJMB030827,SJMB030838,SJMB032893,SJMB031131,SJMB031227","control":"SJMB030488,SJMB030825,SJMB031110","input_file":"/Users/rpaul1/pp_data/files/hg38/sjmb12/rnaseq/geneCounts.txt"}' && time echo $json | target/release/DEanalysis
-// cd .. && cargo build --release && cat ~/sjpp/test.txt | target/release/DEanalysis
+// cd .. && cargo build --release && time cat ~/sjpp/test.txt | target/release/DEanalysis
 #![allow(non_snake_case)]
 use json;
 use nalgebra::base::dimension::Const;
@@ -15,13 +15,46 @@ use statrs::statistics::Data;
 use statrs::statistics::Distribution;
 use statrs::statistics::Median;
 use std::cmp::Ordering;
-use std::path::Path;
+use std::fs::File;
+use std::io::Read;
 use std::str::FromStr;
+use std::sync::{Arc, Mutex}; // Multithreading library
+use std::thread;
 use std::time::Instant;
 //use std::cmp::Ordering;
 //use std::env;
 use std::io;
 //mod stats_functions; // Importing Wilcoxon function from stats_functions.rs
+const PAR_CUTOFF: usize = 100000; // Cutoff for triggering multithreading processing of data
+
+//const PAR_CUTOFF: usize = 1000000000000000;
+#[allow(non_upper_case_globals)]
+const max_threads: usize = 6; // Max number of threads in case the parallel processing of reads is invoked
+
+fn binary_search(input: &Vec<usize>, y: usize) -> i64 {
+    let input_dup = &input[..];
+    let mut index: i64 = -1;
+    let mut l: usize = 0;
+    let mut r: usize = input_dup.len() - 1;
+    let mut m: usize;
+    while l <= r {
+        m = l + ((r - l) / 2);
+        if y == input_dup[m] {
+            index = m as i64;
+            break;
+        } else if y > input_dup[m] {
+            l = m + 1;
+        }
+        // If x is smaller, ignore right half
+        else {
+            if m == 0 as usize {
+                break;
+            }
+            r = m - 1;
+        }
+    }
+    index
+}
 
 fn input_data(
     filename: &String,
@@ -34,9 +67,9 @@ fn input_data(
     Vec<String>,
     Vec<String>,
 ) {
-    // Build the CSV reader and iterate over each record.
-    let path = Path::new(filename);
-    let mut rdr = csv::Reader::from_path(path).unwrap();
+    let input_time = Instant::now();
+    //let mut rdr = csv::Reader::from_path(path).unwrap();
+    let mut file = File::open(filename).unwrap();
     let mut num_lines: usize = 0;
     let mut input_vector: Vec<f64> = Vec::with_capacity(500 * 65000);
     let mut gene_names: Vec<String> = Vec::with_capacity(65000);
@@ -44,11 +77,12 @@ fn input_data(
     let mut num_columns: usize = 0;
 
     // Check headers for samples
-    let header_line = rdr.headers().unwrap();
-    let mut headers: Vec<&str> = Vec::with_capacity(1500);
-    for field in header_line.iter() {
-        headers = field.split('\t').collect::<Vec<&str>>();
-    }
+    let mut buffer = String::new();
+    file.read_to_string(&mut buffer).unwrap();
+    // Check headers for samples
+    let lines: Vec<&str> = buffer.split('\n').collect::<Vec<&str>>();
+    let total_lines = lines.len();
+    let headers: Vec<&str> = lines[0].split('\t').collect::<Vec<&str>>();
     //println!("headers:{:?}", headers);
     let mut case_indexes_original: Vec<usize> = Vec::with_capacity(case_list.len());
     let mut control_indexes_original: Vec<usize> = Vec::with_capacity(control_list.len());
@@ -68,6 +102,7 @@ fn input_data(
             }
         }
     }
+    let num_cases = case_list.len();
 
     for item in control_list {
         //println!("item:{}", item);
@@ -80,70 +115,223 @@ fn input_data(
             }
         }
     }
+    let num_controls = control_list.len();
     //println!("case_indexes_original:{:?}", case_indexes_original);
     //println!("control_indexes_original:{:?}", control_indexes_original);
-
+    case_indexes_original.sort();
+    case_indexes_original.dedup();
+    control_indexes_original.sort();
+    control_indexes_original.dedup();
     let mut case_indexes: Vec<usize> = Vec::with_capacity(case_list.len());
     let mut control_indexes: Vec<usize> = Vec::with_capacity(control_list.len());
-    for result in rdr.records() {
-        // The iterator yields Result<StringRecord, Error>, so we check the
-        // error here.
-        let record = result.unwrap();
-        //println!("record:{:?}", record);
-        let mut index = 0;
-        for field in record[0].split('\t').collect::<Vec<&str>>() {
-            if index == gene_name_index.unwrap() {
-                gene_names.push(field.to_string());
-            } else if index == gene_symbol_index.unwrap() {
-                gene_symbols.push(field.to_string());
-            } else if case_indexes_original.contains(&index) {
-                let num = FromStr::from_str(field);
-                match num {
-                    Ok(n) => {
-                        //println!("n:{}", n);
-                        input_vector.push(n);
-                        if num_lines == 0 {
-                            case_indexes.push(num_columns);
-                            num_columns += 1;
+    if lines.len() * (case_indexes_original.len() + control_indexes_original.len()) < PAR_CUTOFF {
+        // If number of lines is below this number
+        let lines_slice = &lines[..];
+        for line_iter in 1..lines_slice.len() - 1 {
+            // Subtracting 1 from total length of lines_slice because the last one will be empty
+            let line = lines_slice[line_iter];
+            let mut index = 0;
+            for field in line.split('\t').collect::<Vec<&str>>() {
+                if index == gene_name_index.unwrap() {
+                    gene_names.push(field.to_string());
+                } else if index == gene_symbol_index.unwrap() {
+                    gene_symbols.push(field.to_string());
+                } else if binary_search(&case_indexes_original, index) != -1 {
+                    let num = FromStr::from_str(field);
+                    match num {
+                        Ok(n) => {
+                            //println!("n:{}", n);
+                            input_vector.push(n);
+                            if num_lines == 0 {
+                                case_indexes.push(num_columns);
+                                num_columns += 1;
+                            }
+                        }
+                        Err(_n) => {
+                            panic!(
+                                "Number {} in line {} and column {} is not a decimal number",
+                                field,
+                                num_lines + 1,
+                                index + 1
+                            );
                         }
                     }
-                    Err(_n) => {
-                        panic!(
-                            "Number {} in line {} and column {} is not a decimal number",
-                            field,
-                            num_lines + 1,
-                            index + 1
-                        );
+                } else if binary_search(&control_indexes_original, index) != -1 {
+                    let num = FromStr::from_str(field);
+                    match num {
+                        Ok(n) => {
+                            //println!("n:{}", n);
+                            input_vector.push(n);
+                            if num_lines == 0 {
+                                control_indexes.push(num_columns);
+                                num_columns += 1;
+                            }
+                        }
+                        Err(_n) => {
+                            panic!(
+                                "Number {} in line {} and column {} is not a decimal number",
+                                field,
+                                num_lines + 1,
+                                index + 1
+                            );
+                        }
                     }
                 }
-            } else if control_indexes_original.contains(&index) {
-                let num = FromStr::from_str(field);
-                match num {
-                    Ok(n) => {
-                        //println!("n:{}", n);
-                        input_vector.push(n);
-                        if num_lines == 0 {
-                            control_indexes.push(num_columns);
-                            num_columns += 1;
+                index += 1;
+            }
+            num_lines += 1;
+        }
+    } else {
+        // Multithreaded implementation for parsing data in parallel starts from here
+        // Generally in rust one variable only own a data at a time, but `Arc` keyword is special and allows for multiple threads to access the same data.
+        let case_indexes_original = Arc::new(case_indexes_original);
+        let control_indexes_original = Arc::new(control_indexes_original);
+        let buffer = Arc::new(buffer);
+        let case_indexes_temp = Arc::new(Mutex::new(Vec::<usize>::with_capacity(case_list.len())));
+        let control_indexes_temp =
+            Arc::new(Mutex::new(Vec::<usize>::with_capacity(control_list.len())));
+        let num_lines_temp = Arc::new(Mutex::<usize>::new(0));
+        let num_columns_temp = Arc::new(Mutex::<usize>::new(0));
+        let genes_names_temp = Arc::new(Mutex::new(Vec::<String>::new()));
+        let genes_symbols_temp = Arc::new(Mutex::new(Vec::<String>::new()));
+        let input_vector_temp = Arc::new(Mutex::new(Vec::<f64>::new()));
+        let mut handles = vec![]; // Vector to store handle which is used to prevent one thread going ahead of another
+        println!("Number of threads used:{}", max_threads);
+        for thread_num in 0..max_threads {
+            let case_indexes_original = Arc::clone(&case_indexes_original);
+            let control_indexes_original = Arc::clone(&control_indexes_original);
+            let case_indexes_temp = Arc::clone(&case_indexes_temp);
+            let control_indexes_temp = Arc::clone(&control_indexes_temp);
+            let input_vector_temp = Arc::clone(&input_vector_temp);
+            let genes_names_temp = Arc::clone(&genes_names_temp);
+            let genes_symbols_temp = Arc::clone(&genes_symbols_temp);
+            let num_lines_temp = Arc::clone(&num_lines_temp);
+            let num_columns_temp = Arc::clone(&num_columns_temp);
+            let buffer = Arc::clone(&buffer);
+            let handle = thread::spawn(move || {
+                let mut case_indexes_thread: Vec<usize> = Vec::with_capacity(num_cases);
+                let mut control_indexes_thread: Vec<usize> = Vec::with_capacity(num_controls);
+                let mut genes_names_thread: Vec<String> = Vec::with_capacity(65000);
+                let mut genes_symbols_thread: Vec<String> = Vec::with_capacity(65000);
+                let mut input_vector_thread: Vec<f64> = Vec::with_capacity(65000);
+                let mut num_columns_thread: usize = 0;
+                let mut num_lines_thread: usize = 0;
+                let lines: Vec<&str> = buffer.split('\n').collect();
+                //println!("case_indexes_original:{:?}", case_indexes_original);
+                //println!("control_indexes:{:?}", control_indexes);
+                for line_iter in 1..total_lines - 1 {
+                    let remainder: usize = line_iter % max_threads; // Calculate remainder of line number divided by max_threads to decide which thread parses this line
+                    if remainder == thread_num {
+                        //println!("buffer:{}", buffer);
+                        // Thread analyzing a particular line must have the same remainder as the thread_num, this avoids multiple threads from parsing the same line
+                        let line = lines[line_iter];
+                        let mut index = 0;
+                        for field in line.split('\t').collect::<Vec<&str>>() {
+                            if index == gene_name_index.unwrap() {
+                                genes_names_thread.push(field.to_string());
+                            } else if index == gene_symbol_index.unwrap() {
+                                genes_symbols_thread.push(field.to_string());
+                            } else if binary_search(&case_indexes_original, index) != -1 {
+                                let num = FromStr::from_str(field);
+                                match num {
+                                    Ok(n) => {
+                                        //println!("n:{}", n);
+                                        input_vector_thread.push(n);
+                                        if line_iter == 1 {
+                                            case_indexes_thread.push(num_columns_thread);
+                                            num_columns_thread += 1;
+                                        }
+                                    }
+                                    Err(_n) => {
+                                        panic!(
+                                        "Number {} in line {} and column {} is not a decimal number",
+                                        field,
+                                        num_lines_thread + 1,
+                                        index + 1
+                                    );
+                                    }
+                                }
+                            } else if binary_search(&control_indexes_original, index) != -1 {
+                                let num = FromStr::from_str(field);
+                                match num {
+                                    Ok(n) => {
+                                        //println!("n:{}", n);
+                                        input_vector_thread.push(n);
+                                        if line_iter == 1 {
+                                            control_indexes_thread.push(num_columns_thread);
+                                            num_columns_thread += 1;
+                                        }
+                                    }
+                                    Err(_n) => {
+                                        panic!(
+                                        "Number {} in line {} and column {} is not a decimal number",
+                                        field,
+                                        num_lines_thread + 1,
+                                        index + 1
+                                    );
+                                    }
+                                }
+                            }
+                            index += 1;
                         }
-                    }
-                    Err(_n) => {
-                        panic!(
-                            "Number {} in line {} and column {} is not a decimal number",
-                            field,
-                            num_lines + 1,
-                            index + 1
-                        );
+                        num_lines_thread += 1;
                     }
                 }
-            }
-            index += 1;
+                input_vector_temp
+                    .lock()
+                    .unwrap()
+                    .append(&mut input_vector_thread);
+                case_indexes_temp
+                    .lock()
+                    .unwrap()
+                    .append(&mut case_indexes_thread);
+                control_indexes_temp
+                    .lock()
+                    .unwrap()
+                    .append(&mut control_indexes_thread);
+                genes_names_temp
+                    .lock()
+                    .unwrap()
+                    .append(&mut genes_names_thread);
+                genes_symbols_temp
+                    .lock()
+                    .unwrap()
+                    .append(&mut genes_symbols_thread);
+                *num_lines_temp.lock().unwrap() += num_lines_thread;
+                if num_columns_thread > 0 {
+                    *num_columns_temp.lock().unwrap() += num_columns_thread;
+                }
+                drop(input_vector_temp);
+                drop(case_indexes_temp);
+                drop(control_indexes_temp);
+                drop(genes_names_temp);
+                drop(genes_symbols_temp);
+                drop(num_lines_temp);
+                drop(num_columns_temp);
+            });
+            handles.push(handle); // The handle (which contains the thread) is stored in the handles vector
+        }
+        for handle in handles {
+            // Wait for all threads to finish before proceeding further
+            handle.join().unwrap();
         }
-        num_lines += 1;
+        // Combining data from all different threads
+        input_vector.append(&mut *input_vector_temp.lock().unwrap());
+        case_indexes.append(&mut *case_indexes_temp.lock().unwrap());
+        control_indexes.append(&mut *control_indexes_temp.lock().unwrap());
+        gene_names.append(&mut *genes_names_temp.lock().unwrap());
+        gene_symbols.append(&mut *genes_symbols_temp.lock().unwrap());
+
+        num_lines += *num_lines_temp.lock().unwrap();
+        num_columns += *num_columns_temp.lock().unwrap();
     }
     //println!("case_indexes:{:?}", case_indexes);
     //println!("control_indexes:{:?}", control_indexes);
-
+    //println!("num_lines:{}", num_lines);
+    //println!("num_columns:{}", num_columns);
+    //println!("num_lines * num_columns:{}", num_lines * num_columns);
+    //println!("input_vector:{:?}", input_vector.len());
+    println!("Time for inputting data:{:?}", input_time.elapsed());
     let dm = DMatrix::from_row_slice(num_lines, num_columns, &input_vector);
     //println!("dm:{:?}", dm);
     (dm, case_indexes, control_indexes, gene_names, gene_symbols)
@@ -198,6 +386,7 @@ fn main() {
                     let control_list: Vec<&str> = control_string.split(",").collect();
                     let (input_matrix, case_indexes, control_indexes, gene_names, gene_symbols) =
                         input_data(file_name, &case_list, &control_list);
+                    let filtering_time = Instant::now();
                     let (filtered_matrix, lib_sizes, filtered_genes, filtered_gene_symbols) =
                         filter_by_expr(
                             &input_matrix,
@@ -206,10 +395,21 @@ fn main() {
                             gene_names,
                             gene_symbols,
                         );
+                    println!("filtering time:{:?}", filtering_time.elapsed());
                     //println!("filtered_matrix_rows:{:?}", filtered_matrix.nrows());
                     //println!("filtered_matrix_cols:{:?}", filtered_matrix.ncols());
+                    let cpm_normalization_time = Instant::now();
                     let mut normalized_matrix = cpm(&filtered_matrix);
+                    println!(
+                        "cpm normalization time:{:?}",
+                        cpm_normalization_time.elapsed()
+                    );
+                    let tmm_normalization_time = Instant::now();
                     let norm_factors = tmm_normalization(filtered_matrix, &lib_sizes);
+                    println!(
+                        "tmm normalization time:{:?}",
+                        tmm_normalization_time.elapsed()
+                    );
                     //println!("norm_factors:{:?}", norm_factors);
 
                     for col in 0..normalized_matrix.ncols() {
@@ -232,58 +432,154 @@ fn main() {
 
                     //println!("case_indexes:{:?}", case_indexes);
                     //println!("control_indexes:{:?}", control_indexes);
-                    for i in 0..normalized_matrix.nrows() {
-                        let row = normalized_matrix.row(i);
-                        //println!("row:{:?}", row);
-                        let mut treated = Vec::<f64>::new();
-                        let mut control = Vec::<f64>::new();
-                        //println!("conditions:{:?}", conditions);
-                        for j in 0..(case_indexes.len() + control_indexes.len()) {
-                            //println!("row[(0, j)]:{}", row[(0, j)]);
-                            if case_indexes.contains(&j) {
-                                treated.push(row[(0, j)]);
-                                //println!("{},{}", input_data_vec.0[i][j], "Diseased");
-                            } else if control_indexes.contains(&j) {
-                                // + 1 was added because in the input file the first column of thw first row is blank as the first column consists of gene names
-                                control.push(row[(0, j)]);
-                                //println!("{},{}", input_data_vec.0[i][j], "Control");
-                            } else {
-                                panic!("Column {} could not be classified into case/control", j);
+                    let num_normalized_rows = normalized_matrix.nrows();
+                    if normalized_matrix.nrows() * normalized_matrix.ncols() < PAR_CUTOFF {
+                        for i in 0..normalized_matrix.nrows() {
+                            let row = normalized_matrix.row(i);
+                            //println!("row:{:?}", row);
+                            let mut treated = Vec::<f64>::new();
+                            let mut control = Vec::<f64>::new();
+                            //println!("conditions:{:?}", conditions);
+                            for j in 0..(case_indexes.len() + control_indexes.len()) {
+                                //println!("row[(0, j)]:{}", row[(0, j)]);
+                                if case_indexes.contains(&j) {
+                                    treated.push(row[(0, j)]);
+                                    //println!("{},{}", input_data_vec.0[i][j], "Diseased");
+                                } else if control_indexes.contains(&j) {
+                                    // + 1 was added because in the input file the first column of thw first row is blank as the first column consists of gene names
+                                    control.push(row[(0, j)]);
+                                    //println!("{},{}", input_data_vec.0[i][j], "Control");
+                                } else {
+                                    panic!(
+                                        "Column {} could not be classified into case/control",
+                                        j
+                                    );
+                                }
                             }
-                        }
-                        //println!("treated{:?}", treated);
-                        //println!("control{:?}", control);
-                        let p_value = wilcoxon_rank_sum_test(
-                            treated.clone(),
-                            control.clone(),
-                            THRESHOLD,
-                            't',
-                            true,
-                        ); // Setting continuity correction to true in case of normal approximation
-                        let treated_mean = Data::new(treated).mean();
-                        let control_mean = Data::new(control).mean();
-                        if (treated_mean.unwrap() / control_mean.unwrap())
-                            .log2()
-                            .is_nan()
-                            == false
-                            && (treated_mean.unwrap() / control_mean.unwrap())
+                            //println!("treated{:?}", treated);
+                            //println!("control{:?}", control);
+                            let p_value = wilcoxon_rank_sum_test(
+                                treated.clone(),
+                                control.clone(),
+                                THRESHOLD,
+                                't',
+                                true,
+                            ); // Setting continuity correction to true in case of normal approximation
+                            let treated_mean = Data::new(treated).mean();
+                            let control_mean = Data::new(control).mean();
+                            if (treated_mean.unwrap() / control_mean.unwrap())
                                 .log2()
-                                .is_infinite()
+                                .is_nan()
                                 == false
-                        {
-                            p_values.push(PValueIndexes {
-                                index: i,
-                                gene_name: filtered_genes[i].to_owned(),
-                                gene_symbol: filtered_gene_symbols[i].to_owned(),
-                                fold_change: (treated_mean.unwrap() / control_mean.unwrap()).log2(),
-                                p_value: p_value,
+                                && (treated_mean.unwrap() / control_mean.unwrap())
+                                    .log2()
+                                    .is_infinite()
+                                    == false
+                            {
+                                p_values.push(PValueIndexes {
+                                    index: i,
+                                    gene_name: filtered_genes[i].to_owned(),
+                                    gene_symbol: filtered_gene_symbols[i].to_owned(),
+                                    fold_change: (treated_mean.unwrap() / control_mean.unwrap())
+                                        .log2(),
+                                    p_value: p_value,
+                                });
+                            }
+                        }
+                    } else {
+                        // Multithreaded implementation of calculating wilcoxon p-values
+                        let normalized_matrix_temp = Arc::new(normalized_matrix);
+                        let filtered_genes_temp = Arc::new(filtered_genes);
+                        let filtered_gene_symbols_temp = Arc::new(filtered_gene_symbols);
+                        let case_indexes_temp = Arc::new(case_indexes);
+                        let control_indexes_temp = Arc::new(control_indexes);
+                        let p_values_temp = Arc::new(Mutex::new(Vec::<PValueIndexes>::new()));
+                        let mut handles = vec![]; // Vector to store handle which is used to prevent one thread going ahead of another
+                        for thread_num in 0..max_threads {
+                            let normalized_matrix_temp = Arc::clone(&normalized_matrix_temp);
+                            let case_indexes_temp = Arc::clone(&case_indexes_temp);
+                            let control_indexes_temp = Arc::clone(&control_indexes_temp);
+                            let p_values_temp = Arc::clone(&p_values_temp);
+                            let filtered_genes_temp = Arc::clone(&filtered_genes_temp);
+                            let filtered_gene_symbols_temp =
+                                Arc::clone(&filtered_gene_symbols_temp);
+                            let handle = thread::spawn(move || {
+                                let mut p_values_thread: Vec<PValueIndexes> = Vec::with_capacity(
+                                    normalized_matrix_temp.nrows() / max_threads,
+                                );
+                                for i in 0..normalized_matrix_temp.nrows() {
+                                    let remainder: usize = i % max_threads; // Calculate remainder of iteration number divided by max_threads to decide which thread parses the row
+                                    if remainder == thread_num {
+                                        let row = normalized_matrix_temp.row(i);
+                                        //println!("row:{:?}", row);
+                                        let mut treated = Vec::<f64>::new();
+                                        let mut control = Vec::<f64>::new();
+                                        //println!("conditions:{:?}", conditions);
+                                        for j in 0..(case_indexes_temp.len()
+                                            + control_indexes_temp.len())
+                                        {
+                                            //println!("row[(0, j)]:{}", row[(0, j)]);
+                                            if case_indexes_temp.contains(&j) {
+                                                treated.push(row[(0, j)]);
+                                                //println!("{},{}", input_data_vec.0[i][j], "Diseased");
+                                            } else if control_indexes_temp.contains(&j) {
+                                                // + 1 was added because in the input file the first column of thw first row is blank as the first column consists of gene names
+                                                control.push(row[(0, j)]);
+                                                //println!("{},{}", input_data_vec.0[i][j], "Control");
+                                            } else {
+                                                panic!(
+                                        "Column {} could not be classified into case/control",
+                                        j
+                                    );
+                                            }
+                                        }
+                                        //println!("treated{:?}", treated);
+                                        //println!("control{:?}", control);
+                                        let p_value = wilcoxon_rank_sum_test(
+                                            treated.clone(),
+                                            control.clone(),
+                                            THRESHOLD,
+                                            't',
+                                            true,
+                                        ); // Setting continuity correction to true in case of normal approximation
+                                        let treated_mean = Data::new(treated).mean();
+                                        let control_mean = Data::new(control).mean();
+                                        if (treated_mean.unwrap() / control_mean.unwrap())
+                                            .log2()
+                                            .is_nan()
+                                            == false
+                                            && (treated_mean.unwrap() / control_mean.unwrap())
+                                                .log2()
+                                                .is_infinite()
+                                                == false
+                                        {
+                                            p_values_thread.push(PValueIndexes {
+                                                index: i,
+                                                gene_name: filtered_genes_temp[i].to_owned(),
+                                                gene_symbol: filtered_gene_symbols_temp[i]
+                                                    .to_owned(),
+                                                fold_change: (treated_mean.unwrap()
+                                                    / control_mean.unwrap())
+                                                .log2(),
+                                                p_value: p_value,
+                                            });
+                                        }
+                                    }
+                                }
+                                p_values_temp.lock().unwrap().append(&mut p_values_thread);
                             });
+                            handles.push(handle);
                         }
+                        for handle in handles {
+                            // Wait for all threads to finish before proceeding further
+                            handle.join().unwrap();
+                        }
+                        p_values.append(&mut *p_values_temp.lock().unwrap());
                     }
                     //println!("p_values:{:?}", p_values);
                     println!(
                         "Time for running {} wilcoxon tests:{:?}",
-                        normalized_matrix.nrows(),
+                        num_normalized_rows,
                         now2.elapsed()
                     );
                     let adjusted_p_values = adjust_p_values(p_values);
@@ -408,18 +704,62 @@ fn tmm_normalization(
         }
     }
     //println!("ref_column:{}", ref_column);
-    let ref_data = input_matrix.column(ref_column);
-    let ref_lib_size = lib_sizes[ref_column];
+    let num_cols = input_matrix.ncols();
     let mut f: Vec<f64> = Vec::with_capacity(input_matrix.ncols());
-    for col in 0..input_matrix.ncols() {
-        let obs_data = input_matrix.column(col);
-        let obs_lib_size = lib_sizes[col];
-        f.push(calc_factor_tmm(
-            obs_data,
-            &ref_data,
-            ref_lib_size,
-            obs_lib_size,
-        ));
+    if input_matrix.nrows() * input_matrix.ncols() < PAR_CUTOFF {
+        let ref_data = input_matrix.column(ref_column);
+        let ref_lib_size = lib_sizes[ref_column];
+        for col in 0..input_matrix.ncols() {
+            let obs_data = input_matrix.column(col);
+            let obs_lib_size = lib_sizes[col];
+            f.push(calc_factor_tmm(
+                obs_data,
+                &ref_data,
+                ref_lib_size,
+                obs_lib_size,
+            ));
+        }
+    } else {
+        // Multithreaded implementation of TMM normalization
+        let f_temp = Arc::new(Mutex::new(Vec::<f_index>::new()));
+        let lib_sizes_temp = Arc::new(lib_sizes.to_owned());
+        let input_matrix_temp = Arc::new(input_matrix);
+        let mut handles = vec![]; // Vector to store handle which is used to prevent one thread going ahead of another
+        for thread_num in 0..max_threads {
+            let f_temp = Arc::clone(&f_temp);
+            let lib_sizes_temp = Arc::clone(&lib_sizes_temp);
+            let input_matrix_temp = Arc::clone(&input_matrix_temp);
+            let handle = thread::spawn(move || {
+                let mut f_thread: Vec<f_index> =
+                    Vec::with_capacity(input_matrix_temp.ncols() / max_threads);
+                let ref_data = input_matrix_temp.column(ref_column);
+                let ref_lib_size = lib_sizes_temp[ref_column];
+                for col in 0..input_matrix_temp.ncols() {
+                    let remainder: usize = col % max_threads; // Calculate remainder of column number divided by max_threads to decide which thread parses this column
+                    if remainder == thread_num {
+                        let obs_data = input_matrix_temp.column(col);
+                        let obs_lib_size = lib_sizes_temp[col];
+                        f_thread.push(f_index {
+                            f: calc_factor_tmm(obs_data, &ref_data, ref_lib_size, obs_lib_size),
+                            ind: col,
+                        })
+                    }
+                }
+                f_temp.lock().unwrap().append(&mut f_thread);
+            });
+            handles.push(handle);
+        }
+        for handle in handles {
+            // Wait for all threads to finish before proceeding further
+            handle.join().unwrap();
+        }
+        let mut f_orig: Vec<f_index> = Vec::with_capacity(num_cols);
+        f_orig.append(&mut *f_temp.lock().unwrap());
+        // Need to sort vector because the vector will not be ordered accord to ind because of multithreading
+        f_orig
+            .as_mut_slice()
+            .sort_by(|a, b| (a.ind).partial_cmp(&b.ind).unwrap_or(Ordering::Equal));
+        f = f_orig.into_iter().map(|x| x.f).collect::<Vec<f64>>();
     }
     const NATURAL_E: f64 = 2.718281828459;
     let log_f: Vec<f64> = f.clone().into_iter().map(|x| x.log(NATURAL_E)).collect();
@@ -427,6 +767,11 @@ fn tmm_normalization(
     let final_f: Vec<f64> = f.into_iter().map(|x| x / exp_mean_log_f).collect();
     final_f
 }
+#[allow(non_camel_case_types)]
+struct f_index {
+    f: f64,
+    ind: usize,
+}
 
 fn calc_factor_tmm(
     obs_data: Matrix<f64, Dyn, Const<1>, ViewStorage<'_, f64, Dyn, Const<1>, Const<1>, Dyn>>,

package/src/indel.rs

@@ -1,7 +1,7 @@
 // Syntax: cd .. && cargo build --release
 
 // Test case below:
-//Debug syntax: cd .. && cargo build --release && time cat ~/sjpp/test.txt | ~/proteinpaint/rust/target/release/indel
+//Debug syntax: cd .. && cargo build --release && time cat ~/sjpp/test.txt | ~/sjpp/proteinpaint/rust/target/release/indel
 
 // Strictness:
 //   0: No postprocessing, pure indel typing results
@@ -848,7 +848,7 @@ fn main() {
                                     let remainder: usize = iter % max_threads; // Calculate remainder of read number divided by max_threads to decide which thread parses this read
                                                                                //println!("iter:{}", iter);
                                     if remainder == thread_num {
-                                        // Thread analyzing a particular read must have the same remainder as the thread_num, this avoids multiple reads from parsing the same read. Also checking if the read length > 0
+                                        // Thread analyzing a particular read must have the same remainder as the thread_num, this avoids multiple threads from parsing the same read. Also checking if the read length > 0
 
                                         //println!(
                                         //    "start_positions_list:{}",
@@ -1356,7 +1356,12 @@ fn main() {
                     //let mut output_string = "[".to_string();
                     //output_string += &all_alleles.to_string();
                     output_string.pop();
-                    output_string += &"]".to_string();
+                    if output_string.len() == 0 {
+                        // Pass empty JSON "[]" when no reads are passed back to nodejs
+                        output_string = "[]".to_string();
+                    } else {
+                        output_string += &"]".to_string();
+                    }
                     println!("Final_output:{:?}", output_string);
                 }
                 Err(error) => println!("Incorrect json: {}", error),