From 8311650247b4e3958ce25402e5c220891e90cb2b Mon Sep 17 00:00:00 2001
From: Marcel Martin <marcel.martin@scilifelab.se>
Date: Mon, 13 Mar 2023 14:37:35 +0100
Subject: [PATCH] Add operator<< for ksw_extz_t

---
 src/aligner.cpp | 22 ++++++++++++++++++++++
 src/cigar.cpp   |  5 +++++
 src/cigar.hpp   |  2 ++
 3 files changed, 29 insertions(+)

diff --git a/src/aligner.cpp b/src/aligner.cpp
index a041d710..b0adc7a2 100644
--- a/src/aligner.cpp
+++ b/src/aligner.cpp
@@ -11,6 +11,7 @@
 #include <algorithm>
 #include <cassert>
 #include <cstring>  // memset
+#include <iostream>
 #include "ksw2/ksw2.h"
 #include "aligner.hpp"
 
@@ -235,6 +236,27 @@ void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b)
         mat[(m - 1) * m + j] = 0;
 }
 
+std::ostream& operator<<(std::ostream& os, const ksw_extz_t& ez) {
+    os << "ksw_extz_t("
+        //
+        << "\n max:             " << ez.max   // max overall score
+        << "\n coord max_q:     " << ez.max_q  // max extension coordinate
+        << "\n coord max_t:     " << ez.max_t  // max extension coordinate
+
+        << "\n score mqe:       " << ez.mqe // max score when reaching the end of query
+        << "\n mqe_t:           " << ez.mqe_t // coordinate in target corresponding to mqe
+
+        << "\n score mte:       " << ez.mte  // max score when reaching the end of target
+        << "\n mte_q:           " << ez.mte_q // coordinate in query corresponding to mte
+
+        << "\n score both ends: " << ez.score  // max score reaching both ends
+        << "\n cigar:           " << Cigar(ez.cigar, ez.n_cigar)
+        << "\n zdropped:        " << ez.zdropped
+        << "\n reach_end:       " << ez.reach_end
+        << "\n)";
+    return os;
+}
+
 aln_info Aligner::ksw_extend(const std::string& query, const std::string& ref, bool right_align) const {
     int w = -1; // band width; -1 is inf
     int zdrop = -1; // -1 to disable
diff --git a/src/cigar.cpp b/src/cigar.cpp
index 18354112..85eb9508 100644
--- a/src/cigar.cpp
+++ b/src/cigar.cpp
@@ -75,6 +75,11 @@ Cigar::Cigar(const std::string& cig) {
     }
 }
 
+std::ostream& operator<<(std::ostream& os, const Cigar& cigar) {
+    os << cigar.to_string();
+    return os;
+}
+
 std::string compress_cigar(const std::string& ops) {
     char prev = 0;
     int count = 0;
diff --git a/src/cigar.hpp b/src/cigar.hpp
index adfc49aa..00364502 100644
--- a/src/cigar.hpp
+++ b/src/cigar.hpp
@@ -87,6 +87,8 @@ class Cigar {
     std::vector<uint32_t> m_ops;
 };
 
+std::ostream& operator<<(std::ostream& os, const Cigar& cigar);
+
 std::string compress_cigar(const std::string& ops);
 
 #endif