Mostly small things

util/aligner2counts.cpp

@@ -13,6 +13,7 @@
 #include <filesystem>
 #include <unordered_map>
 #include <unordered_set>
+#include <cassert>
 
 const unsigned int FLAG_0 = 0;      // 0 primary alignment
 const unsigned int FLAG_1 = 1;      // 0x1 template having multiple segments in sequencing
@@ -158,7 +159,8 @@ std::pair<float, float> get_seqid_alncov(std::pair<int, int> &alnpos, std::strin
 
     //  Sequence identity only considers aligned region (soft clip region is ignored)
     //  Alignment coverage is calculated w.r.t full read length
-    for (unsigned int i = start; i < end; i++) {
+    assert(end >= 0); // assert that end does not accidentally overflows here
+    for (unsigned int i = start; i < (unsigned int) end; i++) {
         bool is_match;
         if (future_matches > 0) {
             future_matches--;
@@ -196,8 +198,8 @@ std::pair<float, float> get_seqid_alncov(std::pair<int, int> &alnpos, std::strin
         exit(1);
     }
 
-    seq_id = (static_cast<float>(matches) * 100) / (matches+mismatches);
-    alignment_coverage = (static_cast<float>(alignment_length) * 100) / (qual_str.length() + start); // account for variable read length
+    seq_id = (static_cast<float>(matches) * 100.0) / (matches+mismatches);
+    alignment_coverage = (static_cast<float>(alignment_length) * 100.0) / (qual_str.length() + start); // account for variable read length
     // std::cout << matches << " matches " << mismatches << " mismatches " <<  seq_id << " " << alignment_coverage << " " << matches+mismatches << " in alnstats \n";
     return std::make_pair(seq_id, alignment_coverage);
 }
@@ -430,7 +432,7 @@ void process_alignment_line(
     AlnMapids& alnmapids,
     bool& strobealign) {
     if (contigs_map.size() == 0) {
-        std::cerr << "Input sam/bam file doesn't has header. Please provide input file with header \n";
+        std::cerr << "Input sam file doesn't has header. Please provide input file with header \n";
         exit(1);
     }
     std::string currentread_id, contig_id, cigar_str, qual_str, md_str, field;

util/convertfasta_multi2single.cpp

@@ -6,69 +6,85 @@
 #include <chrono>
 #include <filesystem>
 
-
 namespace fs = std::filesystem;
-bool condition_header(std::string &line) {
-    if (line[0] == '>') {
+bool condition_header(std::string &line)
+{
+    if (line[0] == '>')
+    {
         return true;
     }
-    else {
+    else
+    {
         return false;
     }
 }
 
-void get_complete_sequence(std::ifstream &fasta, std::string &line, std::string &sequence) {
+void get_complete_sequence(std::ifstream &fasta, std::string &line, std::string &sequence)
+{
     getline(fasta, line);
-    while (!condition_header(line) && !fasta.eof()) {
+    while (!condition_header(line) && !fasta.eof())
+    {
         sequence.append(line);
         getline(fasta, line);
     }
 }
 
-int main(int argc, char *argv[]) {
+int main(int argc, char *argv[])
+{
 
-    if(argc < 3 || strcmp(argv[1], "--help") == 0 || strcmp(argv[1], "-h") == 0)
+    if (argc < 3 || strcmp(argv[1], "--help") == 0 || strcmp(argv[1], "-h") == 0)
     {
         std::cout << "Usage: convertfasta_multi2single input.fasta outdir min_length (optional, int) --length (print length, optional) \n";
         return EXIT_SUCCESS;
     }
-
-    else {
+
+    else
+    {
         auto start = std::chrono::high_resolution_clock::now();
         std::string contigs_sequences = argv[1];
-        auto pos = contigs_sequences.find_last_of ('/');
+        auto pos = contigs_sequences.find_last_of('/');
         std::string outname;
-        if (pos != std::string::npos) {
-            outname = contigs_sequences.substr(pos+1);
-        } else {
+        if (pos != std::string::npos)
+        {
+            outname = contigs_sequences.substr(pos + 1);
+        }
+        else
+        {
             outname = contigs_sequences;
         }
-    
+
         std::string dir = argv[2];
-        if (!fs::exists(dir)) {
-            if (!fs::create_directories(dir)) {
+        if (!fs::exists(dir))
+        {
+            if (!fs::create_directories(dir))
+            {
                 std::cerr << "Error: Unable to create output directory!" << "\n";
                 return 1;
             }
         }
         unsigned int min_length = 0;
-        bool return_length = 0;
+        bool return_length = false;
         std::ofstream length_file;
-        for (int i = 3; i < argc; ++i) {
-            if (strcmp(argv[i], "--length") == 0) {
+        for (int i = 3; i < argc; ++i)
+        {
+            if (strcmp(argv[i], "--length") == 0)
+            {
                 return_length = true;
-                length_file.open(dir +"/contig_length");
-            } else {
+                length_file.open(dir + "/contig_length");
+            }
+            else
+            {
                 min_length = std::stoi(argv[i]);
             }
         }
 
         std::ifstream fasta(contigs_sequences);
-        std::cout<<"Input file: " << contigs_sequences << "\n";
-        std::cout<<"Output directory: " << dir << "\n";
+        std::cout << "Input file: " << contigs_sequences << "\n";
+        std::cout << "Output directory: " << dir << "\n";
         std::ofstream outfile(dir + "/single_" + outname);
 
-        if (!fasta.is_open()) {
+        if (!fasta.is_open())
+        {
             std::cerr << "Error: Unable to open Fasta file!" << "\n";
             return 1;
         }
@@ -78,9 +94,10 @@ int main(int argc, char *argv[]) {
         getline(fasta, line);
         std::string header;
         unsigned int sequence_counter = 0;
-        while (condition_header(line)) {
+        while (condition_header(line))
+        {
             header = line;
-           
+
             // Find the start position, which is after '>'
             size_t start_pos = line.find('>') + 1;
 
@@ -92,29 +109,34 @@ int main(int argc, char *argv[]) {
             sequence = "";
             get_complete_sequence(fasta, line, sequence);
 
-            if (!sequence.empty()) {
-                if (sequence.length() >= min_length) {
+            if (!sequence.empty())
+            {
+                if (sequence.length() >= min_length)
+                {
                     outfile << header << "\n";
                     outfile << sequence << "\n";
-                    if (return_length==1) {
+                    if (return_length)
+                    {
                         length_file << seq_id << "\t" << sequence.length() << "\n";
                     }
                 }
             }
-            else {
+            else
+            {
                 std::cerr << "empty sequence for a header" << "\n";
                 return 1;
             }
             sequence_counter++;
         }
         outfile.close();
-        if (return_length && length_file.is_open()) {
+        if (return_length && length_file.is_open())
+        {
             length_file.close();
         }
         std::cout << sequence_counter << " sequences processed \n";
         auto stop = std::chrono::high_resolution_clock::now();
         auto duration = std::chrono::duration_cast<std::chrono::seconds>(stop - start);
         std::cout << duration.count() << " seconds\n";
-        return  EXIT_SUCCESS;
+        return EXIT_SUCCESS;
     }
 }

util/get_sequence_bybin.cpp

@@ -1,4 +1,3 @@
-#include<bits/stdc++.h>
 #include <iostream>
 #include <fstream>
 #include <sstream>
@@ -11,7 +10,7 @@
 
 namespace fs = std::filesystem;
 
-bool condition_header(std::ifstream &fasta, std::string &line) {
+bool condition_header(std::string &line) {
     if (line[0] == '>') {
         return true;
     }
@@ -32,7 +31,7 @@ bool line_check(std::ifstream &fasta, std::string &line) {
 
 void get_complete_sequence(std::ifstream &fasta, std::string &line, std::string &sequence) {
     fasta >> line;
-    while (!condition_header(fasta, line) && !fasta.eof()) {
+    while (!condition_header(line) && !fasta.eof()) {
         if (line_check(fasta, line)) {
             sequence.append(line);
             fasta >> line;
@@ -114,7 +113,7 @@ int main(int argc, char *argv[]) {
         }
 
         fastaFile >> line;
-        while (condition_header(fastaFile, line)) {
+        while (condition_header(line)) {
             sequence = "";
             auto range = bins_ids.equal_range(line.substr(1,-1));
             if (range.first != range.second) {
@@ -137,7 +136,7 @@ int main(int argc, char *argv[]) {
             }
             else {
                 fastaFile >> line;
-                while (!condition_header(fastaFile, line) && !fastaFile.eof()) {
+                while (!condition_header(line) && !fastaFile.eof()) {
                     fastaFile >> line;
                 }
             }