Some small include cleanup

ablab · Apr 8, 2024 · 2e25adf · 2e25adf
1 parent d28746b
commit 2e25adf
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Showing 11 changed files with 25 additions and 15 deletions.
diff --git a/src/common/kmer_index/kmer_counting.hpp b/src/common/kmer_index/kmer_counting.hpp
@@ -7,11 +7,16 @@
 
 #pragma once
 
+#include "ph_map/storing_traits.hpp"
+#include "io/reads/read_processor.hpp" // FIXME: remove use of ReadProcessor
+
+#include "sequence/rtseq.hpp"
+#include "sequence/sequence.hpp"
+
 #include "adt/cyclichash.hpp"
 #include "adt/hll.hpp"
 #include "adt/cqf.hpp"
-#include "ph_map/storing_traits.hpp"
-#include "io/reads/read_processor.hpp"
+
 #include "utils/parallel/openmp_wrapper.h"
 #include "utils/logger/logger.hpp"
 

diff --git a/src/common/kmer_index/kmer_mph/kmer_index.hpp b/src/common/kmer_index/kmer_mph/kmer_index.hpp
@@ -7,7 +7,6 @@
 //* See file LICENSE for details.
 //***************************************************************************
 
-#include "kmer_index_traits.hpp"
 #include "kmer_buckets.hpp"
 
 #include <boomphf/BooPHF.h>

diff --git a/src/common/kmer_index/kmer_mph/kmer_index_builder.hpp b/src/common/kmer_index/kmer_mph/kmer_index_builder.hpp
@@ -15,10 +15,7 @@
 #include "io/binary/binary.hpp"
 
 #include "utils/parallel/openmp_wrapper.h"
-#include "utils/memory_limit.hpp"
 #include "utils/logger/logger.hpp"
-#include "utils/filesystem/path_helper.hpp"
-#include "utils/filesystem/file_limit.hpp"
 #include "utils/perf/timetracer.hpp"
 
 #include "adt/kmer_vector.hpp"

diff --git a/src/common/kmer_index/kmer_mph/kmer_splitters.hpp b/src/common/kmer_index/kmer_mph/kmer_splitters.hpp
@@ -9,7 +9,9 @@
 #pragma once
 
 #include "kmer_splitter.hpp"
-#include "io/reads/io_helper.hpp"
+#include "io/reads/read_stream_vector.hpp"
+#include "sequence/rtseq.hpp"
+#include "sequence/sequence.hpp"
 #include "adt/iterator_range.hpp"
 
 namespace kmers {

diff --git a/src/common/kmer_index/ph_map/cqf_hash_map.hpp b/src/common/kmer_index/ph_map/cqf_hash_map.hpp
@@ -1,11 +1,12 @@
-#pragma once
 //***************************************************************************
 //* Copyright (c) 2023-2024 SPAdes team
 //* Copyright (c) 2020-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************
 
+#pragma once
+
 #include "perfect_hash_map.hpp"
 #include "adt/cqf.hpp"
 

diff --git a/src/common/kmer_index/ph_map/kmer_maps.hpp b/src/common/kmer_index/ph_map/kmer_maps.hpp
@@ -1,11 +1,12 @@
-#pragma once
 //***************************************************************************
 //* Copyright (c) 2023-2024 SPAdes team
 //* Copyright (c) 2020-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************
 
+#pragma once
+
 #include "perfect_hash_map.hpp"
 #include "io/kmers/kmer_iterator.hpp"
 #include "utils/logger/logger.hpp"

diff --git a/src/common/kmer_index/ph_map/perfect_hash_map.hpp b/src/common/kmer_index/ph_map/perfect_hash_map.hpp
@@ -1,4 +1,3 @@
-#pragma once
 //***************************************************************************
 //* Copyright (c) 2023-2024 SPAdes team
 //* Copyright (c) 2015-2022 Saint Petersburg State University
@@ -7,15 +6,18 @@
 //* See file LICENSE for details.
 //***************************************************************************
 
+#pragma once
+
 #include "key_with_hash.hpp"
 #include "storing_traits.hpp"
 #include "kmer_index/kmer_mph/kmer_index.hpp"
+#include "kmer_index/kmer_mph/kmer_index_traits.hpp"
+
 #include "io/binary/binary.hpp"
-#include "utils/verify.hpp"
 #include "utils/parallel/openmp_wrapper.h"
+
 #include <vector>
 #include <cstdlib>
-#include <cstdint>
 
 namespace kmers {
 

diff --git a/src/common/kmer_index/ph_map/perfect_hash_map_builder.hpp b/src/common/kmer_index/ph_map/perfect_hash_map_builder.hpp
@@ -1,11 +1,12 @@
-#pragma once
 //***************************************************************************
 //* Copyright (c) 2023-2024 SPAdes team
 //* Copyright (c) 2016-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************
 
+#pragma once
+
 #include "perfect_hash_map.hpp"
 #include "kmer_maps.hpp"
 #include "cqf_hash_map.hpp"

diff --git a/src/projects/hammer/kmer_data.hpp b/src/projects/hammer/kmer_data.hpp
@@ -10,10 +10,11 @@
 #define __HAMMER_KMER_DATA_HPP__
 
 #include "kmer_stat.hpp"
-#include "adt/array_vector.hpp"
 
 #include "kmer_index/kmer_mph/kmer_index.hpp"
+#include "kmer_index/kmer_mph/kmer_index_traits.hpp"
 #include "utils/logger/logger.hpp"
+#include "adt/array_vector.hpp"
 
 #include <vector>
 

diff --git a/src/projects/ionhammer/kmer_data.hpp b/src/projects/ionhammer/kmer_data.hpp
@@ -12,6 +12,7 @@
 
 #include "config_struct.hpp"
 #include "kmer_index/kmer_mph/kmer_index.hpp"
+#include "kmer_index/kmer_mph/kmer_index_traits.hpp"
 #include "utils/logger/logger.hpp"
 
 #include "hkmer.hpp"

diff --git a/src/projects/mts/contig_abundance.cpp b/src/projects/mts/contig_abundance.cpp
@@ -6,8 +6,8 @@
 //***************************************************************************
 
 #include "contig_abundance.hpp"
-#include "kmer_index/kmer_mph/kmer_splitters.hpp"
 #include "math/xmath.h"
+#include "utils/stl_utils.hpp"
 
 namespace debruijn_graph {