From 80afc8f9991510951bc9b452ee9f9e800d81a929 Mon Sep 17 00:00:00 2001
From: Lydia Buntrock <lydia.buntrock@fu-berlin.de>
Date: Wed, 17 Feb 2021 14:00:09 +0100
Subject: [PATCH] [MISC] Move as many includes from header files to the
 corresponding cpp files to shorten the (re)build time.

Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>
---
 include/detect_breakends/junction_detection.hpp       | 11 +++--------
 .../find_deletions/deletion_finding_and_printing.hpp  |  8 +-------
 src/detect_breakends.cpp                              |  1 +
 src/detect_breakends/junction_detection.cpp           |  9 +++++++++
 src/find_deletions.cpp                                |  1 +
 src/find_deletions/deletion_finding_and_printing.cpp  |  8 +++++---
 6 files changed, 20 insertions(+), 18 deletions(-)

diff --git a/include/detect_breakends/junction_detection.hpp b/include/detect_breakends/junction_detection.hpp
index 688d8860..99f4242d 100644
--- a/include/detect_breakends/junction_detection.hpp
+++ b/include/detect_breakends/junction_detection.hpp
@@ -1,14 +1,9 @@
 #pragma once
 
-#include <seqan3/core/debug_stream.hpp>
-#include <seqan3/io/alignment_file/input.hpp>   // SAM/BAM support
-#include <seqan3/io/sequence_file/output.hpp>   // FASTA support
+#include <seqan3/std/filesystem>    // for filesystem
+#include <vector>
 
-#include "detect_breakends/bam_functions.hpp"   // for hasFlag* functions
-#include "junction.hpp"                         // for class junction
-#include "cluster.hpp"                          // for class cluster
-#include "detect_breakends/aligned_segment.hpp" // for struct aligned_segment
-#include "method_enums.hpp"                     // for enum clustering_methods
+#include "method_enums.hpp"         // for enum clustering_methods
 
 /*! \brief Detects junctions between distant genomic positions by analyzing an alignment file (sam/bam). The detected
  *         junctions are printed on stdout and insertion alleles are stored in a fasta file.
diff --git a/include/find_deletions/deletion_finding_and_printing.hpp b/include/find_deletions/deletion_finding_and_printing.hpp
index 405ef7e6..a238be60 100644
--- a/include/find_deletions/deletion_finding_and_printing.hpp
+++ b/include/find_deletions/deletion_finding_and_printing.hpp
@@ -1,13 +1,7 @@
 #pragma once
 
 #include <seqan3/std/filesystem>
-#include <seqan3/core/debug_stream.hpp>
-#include <seqan3/io/stream/concept.hpp>
-#include <fstream>
-#include <iostream>
-#include <vector>
-
-#include "junction.hpp"
+#include <ostream>
 
 /*! \brief Detects deletions out of the junction file.
  *
diff --git a/src/detect_breakends.cpp b/src/detect_breakends.cpp
index 76e09822..bd91b954 100644
--- a/src/detect_breakends.cpp
+++ b/src/detect_breakends.cpp
@@ -1,4 +1,5 @@
 #include <seqan3/argument_parser/argument_parser.hpp>
+#include <seqan3/core/debug_stream.hpp>
 #include <seqan3/range/views/get.hpp>
 
 #include "detect_breakends/junction_detection.hpp"
diff --git a/src/detect_breakends/junction_detection.cpp b/src/detect_breakends/junction_detection.cpp
index 37f95dbd..874b1c64 100644
--- a/src/detect_breakends/junction_detection.cpp
+++ b/src/detect_breakends/junction_detection.cpp
@@ -1,5 +1,14 @@
 #include "detect_breakends/junction_detection.hpp"
 
+#include <seqan3/core/debug_stream.hpp>
+#include <seqan3/io/alignment_file/input.hpp>   // SAM/BAM support
+#include <seqan3/io/sequence_file/output.hpp>   // FASTA support
+
+#include "cluster.hpp"                          // for class Cluster
+#include "detect_breakends/aligned_segment.hpp" // for struct AlignedSegment
+#include "detect_breakends/bam_functions.hpp"   // for hasFlag* functions
+#include "junction.hpp"                         // for class Jnction
+
 using seqan3::operator""_cigar_op;
 using seqan3::operator""_tag;
 
diff --git a/src/find_deletions.cpp b/src/find_deletions.cpp
index 1b22aba0..cb4dee00 100644
--- a/src/find_deletions.cpp
+++ b/src/find_deletions.cpp
@@ -1,4 +1,5 @@
 #include <seqan3/argument_parser/argument_parser.hpp>
+#include <seqan3/core/debug_stream.hpp>
 
 #include "find_deletions/deletion_finding_and_printing.hpp"
 
diff --git a/src/find_deletions/deletion_finding_and_printing.cpp b/src/find_deletions/deletion_finding_and_printing.cpp
index f5c8f981..5e3aa3ac 100644
--- a/src/find_deletions/deletion_finding_and_printing.cpp
+++ b/src/find_deletions/deletion_finding_and_printing.cpp
@@ -1,7 +1,9 @@
-#include <fstream>
-
 #include "find_deletions/deletion_finding_and_printing.hpp"
-#include "variant_parser/variant_record.hpp"
+
+#include <iostream> // for std::cout
+
+#include "junction.hpp"                         // for class Junction
+#include "variant_parser/variant_record.hpp"    // for class variant_header
 
 /*! \brief Reads the input junction file and stores the junctions in a vector.
  *