iwyu

Author: andrewdavidsmith

GenomicRegion.cpp

@@ -21,11 +21,15 @@
  */
 
 #include "GenomicRegion.hpp"
-
-#include <exception>
+#include "smithlab_os.hpp"
 
 #include <cassert>
+#include <cctype>
+#include <cstdlib>
 #include <fstream>
+#include <limits>
+#include <sstream>
+#include <stdexcept>
 #include <unordered_map>
 
 using std::ostringstream;
@@ -136,8 +140,6 @@ bool SimpleGenomicRegion::operator!=(const SimpleGenomicRegion &rhs) const {
   return (chrom != rhs.chrom || start != rhs.start || end != rhs.end);
 }
 
-#include <iostream>
-
 unordered_map<string, chrom_id_type> GenomicRegion::fw_table_in;
 unordered_map<chrom_id_type, string> GenomicRegion::fw_table_out;
 

GenomicRegion.hpp

@@ -24,19 +24,20 @@
 #ifndef GENOMIC_REGION_HPP
 #define GENOMIC_REGION_HPP
 
-#include "smithlab_os.hpp"
 #include "smithlab_utils.hpp"
 
+#include <algorithm>
 #include <fstream>
-#include <limits>
+#include <iterator>
+#include <stdio.h>
 #include <string>
 #include <unordered_map>
+#include <utility>
 #include <vector>
+class GenomicRegion;
 
 typedef unsigned chrom_id_type;
 
-class GenomicRegion;
-
 class SimpleGenomicRegion {
 public:
   SimpleGenomicRegion() : chrom(assign_chrom("(null)")), start(0), end(0) {}

MappedRead.cpp

@@ -21,11 +21,11 @@
  */
 
 #include "MappedRead.hpp"
-#include "smithlab_utils.hpp"
 
 #include <algorithm>
-#include <fstream>
+#include <cctype>
 #include <sstream>
+#include <stdexcept>
 #include <string>
 
 using std::runtime_error;

MappedRead.hpp

@@ -24,6 +24,8 @@
 #define MAPPED_READ_HPP
 
 #include "GenomicRegion.hpp"
+#include <cstdio>
+#include <string>
 
 struct MappedRead {
   MappedRead() {}

OptionParser.cpp

@@ -22,20 +22,18 @@
  */
 
 #include "OptionParser.hpp"
+#include "smithlab_utils.hpp"
 
+#include <algorithm>
 #include <cassert>
 #include <cctype>
 #include <cstdlib>
-#include <cstring>
-#include <exception>
 #include <fstream>
-#include <functional>
 #include <iomanip>
 #include <iterator>
 #include <regex>
 #include <sstream>
-
-#include "smithlab_utils.hpp"
+#include <stdexcept>
 
 using std::begin;
 using std::end;

OptionParser.hpp

@@ -19,6 +19,7 @@
 #ifndef OPTION_PARSER_HPP
 #define OPTION_PARSER_HPP
 
+#include <cstddef>
 #include <limits>
 #include <string>
 #include <vector>

QualityScore.cpp

@@ -22,8 +22,9 @@
 
 #include "QualityScore.hpp"
 
-#include "smithlab_utils.hpp"
+#include <cctype>
 #include <fstream>
+#include <stdexcept>
 
 using std::runtime_error;
 using std::string;

QualityScore.hpp

@@ -25,6 +25,7 @@
 
 #include <algorithm>
 #include <cmath>
+#include <cstddef>
 #include <string>
 
 ////////////////////////////////////////////////////////////////////////

bisulfite_utils.cpp

@@ -22,14 +22,12 @@
  */
 
 #include "bisulfite_utils.hpp"
+#include <cctype>
 #include <cstdlib>
-#include <iostream>
 #include <random>
 
-using std::string;
-
-void bisulfite_treatment(std::mt19937 &generator, string &seq, double bs_rate,
-                         double meth_rate) {
+void bisulfite_treatment(std::mt19937 &generator, std::string &seq,
+                         double bs_rate, double meth_rate) {
 
   std::uniform_real_distribution<double> unif(0.0, 1.0);
 

chromosome_utils.cpp

@@ -21,8 +21,16 @@
  */
 
 #include "chromosome_utils.hpp"
+#include "GenomicRegion.hpp"
+#include "smithlab_os.hpp"
 
+#include <algorithm>
+#include <cassert>
 #include <cctype>
+#include <cmath>
+#include <cstdlib>
+#include <fstream>
+#include <iterator>
 #include <stdexcept>
 #include <string>
 #include <unordered_map>