Adding the apply_cigar function to cigar_utils.hpp and cpp

Author: andrewdavidsmith

cigar_utils.cpp

@@ -0,0 +1,59 @@
+/* Copyright (C) 2019 Andrew D. Smith
+ *
+ * Authors: Andrew D. Smith
+ *
+ * This is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU General Public License as published by the Free Software
+ * Foundation, either version 3 of the License, or (at your option) any later
+ * version.
+ *
+ * This software is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+ * details.
+ */
+
+#include "cigar_utils.hpp"
+
+#include <exception>
+#include <sstream>
+#include <string>
+
+using std::string;
+using std::to_string;
+using std::runtime_error;
+
+void
+apply_cigar(const string &cigar, string &to_inflate,
+            const char inflation_symbol) {
+  std::istringstream iss(cigar);
+
+  string inflated_seq;
+  size_t n;
+  char op;
+  size_t i = 0;
+  auto to_inflate_beg = std::begin(to_inflate);
+  while (iss >> n >> op) {
+    if (consumes_reference(op) && consumes_query(op)) {
+      inflated_seq.append(to_inflate_beg + i, to_inflate_beg + i + n);
+      i += n;
+    }
+    else if (consumes_query(op)) {
+      // no addition of symbols to query
+      i += n;
+    }
+    else if (consumes_reference(op)) {
+      inflated_seq.append(n, inflation_symbol);
+      // no increment of index within query
+    }
+  }
+
+  // sum of total M/I/S/=/X/N operations must equal length of seq
+  const size_t orig_len = to_inflate.length();
+  if (i != orig_len)
+    throw runtime_error("inconsistent number of qseq ops in cigar: " +
+                        to_inflate + " "  + cigar + " " +
+                        to_string(i) + " " +
+                        to_string(orig_len));
+  to_inflate.swap(inflated_seq);
+}

cigar_utils.hpp

@@ -15,9 +15,12 @@
 
 #ifndef CIGAR_UTILS_HPP
 #define CIGAR_UTILS_HPP
+
 #include <algorithm>
+#include <cctype> // isdigit
+#include <string>
 
-bool
+inline bool
 consumes_query(const char op) {
   return ((op == 'M') ||
           (op == 'I') ||
@@ -26,7 +29,7 @@ consumes_query(const char op) {
           (op == 'X'));
 }
 
-bool
+inline bool
 consumes_reference(const char op) {
   return ((op == 'M') ||
           (op == 'D') ||
@@ -330,4 +333,8 @@ uncompress_cigar(T1 c_itr, const T1 c_end, T2 &cigar) {
   }
 }
 
+void
+apply_cigar(const std::string &cigar, std::string &to_inflate,
+            const char inflation_symbol = 'N');
+
 #endif