src/common.hpp and src/abismal.cpp: fixing missing include info

Author: andrewdavidsmith

src/abismal.cpp

@@ -22,7 +22,6 @@
 #include "dna_four_bit.hpp"
 #include "dna_four_bit_bisulfite.hpp"
 #include "popcnt.hpp"
-#include "sam_flags.hpp"
 
 #include "OptionParser.hpp"
 

src/common.hpp

@@ -12,8 +12,14 @@
  */
 
 #include <algorithm>
+#include <cstddef>
+#include <cstdint>
 #include <cstdlib>
 #include <iomanip>
+#include <iterator>
+#include <sstream>
+#include <string>
+#include <vector>
 
 template <typename T>
 inline auto
@@ -70,3 +76,45 @@ struct progress_bar {
 
   static const std::size_t max_bar_width = 72;
 };
+
+// from 30 April 2020 SAM documentation
+// 1    0x1   template having multiple segments in sequencing
+// 2    0x2   each segment properly aligned according to the aligner
+// 4    0x4   segment unmapped
+// 8    0x8   next segment in the template unmapped
+// 16   0x10  SEQ being reverse complemented
+// 32   0x20  SEQ of the next segment in the template being reverse complemented
+// 64   0x40  the first segment in the template
+// 128  0x80  the last segment in the template
+// 256  0x100 secondary alignment
+// 512  0x200 not passing filters, such as platform/vendor quality controls
+// 1024 0x400 PCR or optical duplicate
+// 2048 0x800 supplementary alignment
+
+namespace samflags {
+// ADS: names of flags adjusted to how we typically interpret
+static const std::uint16_t read_paired = 0x1;
+static const std::uint16_t read_pair_mapped = 0x2;
+static const std::uint16_t read_unmapped = 0x4;
+static const std::uint16_t mate_unmapped = 0x8;
+static const std::uint16_t read_rc = 0x10;
+static const std::uint16_t mate_rc = 0x20;
+static const std::uint16_t template_first = 0x40;
+static const std::uint16_t template_last = 0x80;
+static const std::uint16_t secondary_aln = 0x100;
+static const std::uint16_t below_quality = 0x200;
+static const std::uint16_t pcr_duplicate = 0x400;
+static const std::uint16_t supplementary_aln = 0x800;
+constexpr auto
+check(const std::uint16_t to_check, const std::uint16_t &f) -> bool {
+  return to_check & f;
+}
+constexpr auto
+set(std::uint16_t &to_set, const std::uint16_t f) {
+  to_set |= f;
+}
+constexpr auto
+unset(std::uint16_t &to_unset, const std::uint16_t f) {
+  to_unset &= ~f;
+}
+}  // namespace samflags