remove unnecessary includes

TravisWheelerLab · Dec 9, 2024 · 70704a3 · 70704a3
1 parent b9fbb6d
commit 70704a3
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Showing 30 changed files with 1 addition and 79 deletions.
diff --git a/src/AwFmCreate.c b/src/AwFmCreate.c
@@ -1,14 +1,9 @@
-#include "AwFmCreate.h"
-
 #include <stdlib.h>
 #include <string.h>
-
 #include "AwFmFile.h"
 #include "AwFmIndex.h"
 #include "AwFmIndexStruct.h"
 #include "AwFmLetter.h"
-#include "AwFmSearch.h"
-#include "AwFmSimdConfig.h"
 #include "AwFmSuffixArray.h"
 #include "FastaVector.h"
 #include "divsufsort64.h"

diff --git a/src/AwFmFile.c b/src/AwFmFile.c
@@ -5,13 +5,11 @@
 #define _XOPEN_SOURCE 500
 
 #include "AwFmFile.h"
-
 #include <stdbool.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 #include <unistd.h>
-
 #include "AwFmIndex.h"
 #include "AwFmIndexStruct.h"
 #include "AwFmSuffixArray.h"

diff --git a/src/AwFmFile.h b/src/AwFmFile.h
@@ -3,7 +3,6 @@
 
 #include <stdbool.h>
 #include <stdint.h>
-
 #include "AwFmIndexStruct.h"
 
 /*

diff --git a/src/AwFmIndex.h b/src/AwFmIndex.h
@@ -5,7 +5,6 @@
 #include <stdint.h>
 #include <stdio.h>
 #include <stdlib.h>
-
 #include "FastaVector.h"
 
 #ifdef __cplusplus

diff --git a/src/AwFmIndexStruct.c b/src/AwFmIndexStruct.c
@@ -1,8 +1,6 @@
 #include "AwFmIndexStruct.h"
-
 #include <stdlib.h>
 #include <string.h>
-
 #include "AwFmIndex.h"
 #include "FastaVector.h"
 

diff --git a/src/AwFmIndexStruct.h b/src/AwFmIndexStruct.h
@@ -4,7 +4,6 @@
 #include <stdbool.h>
 #include <stdint.h>
 #include <stdio.h>
-
 #include "AwFmIndex.h"
 
 #define AW_FM_CURRENT_VERSION_NUMBER 8

diff --git a/src/AwFmKmerTable.c b/src/AwFmKmerTable.c
@@ -1,7 +1,5 @@
 #include "AwFmKmerTable.h"
-
 #include "AwFmLetter.h"
-#include "AwFmSearch.h"
 
 bool awFmQueryCanUseKmerTable(const struct AwFmIndex *_RESTRICT_ const index,
                               const char *_RESTRICT_ const kmer,

diff --git a/src/AwFmKmerTable.h b/src/AwFmKmerTable.h
@@ -2,7 +2,6 @@
 #define AW_FM_KMER_TABLE_H
 
 #include <stdint.h>
-
 #include "AwFmIndexStruct.h"
 
 /*

diff --git a/src/AwFmLetter.c b/src/AwFmLetter.c
@@ -1,9 +1,5 @@
 #include "AwFmLetter.h"
-#include "AwFmIndexStruct.h"
-
 #include <ctype.h>
-#include <stdlib.h>
-#include <time.h>
 
 uint8_t awFmAsciiNucleotideToLetterIndex(const uint8_t asciiLetter) {
   uint8_t toLowerCase = asciiLetter | 0x20;

diff --git a/src/AwFmLetter.h b/src/AwFmLetter.h
@@ -2,7 +2,6 @@
 #define AW_FM_LETTER_H
 
 #include <stdint.h>
-
 #include "AwFmIndexStruct.h"
 
 /*

diff --git a/src/AwFmOccurrence.c b/src/AwFmOccurrence.c
@@ -1,7 +1,5 @@
-#include "AwFmOccurrence.h"
-
 #include <stdbool.h>
-
+#include "AwFmOccurrence.h"
 #include "AwFmIndex.h"
 #include "AwFmLetter.h"
 

diff --git a/src/AwFmOccurrence.h b/src/AwFmOccurrence.h
@@ -2,7 +2,6 @@
 #define AW_FM_OCCURANCE_H
 
 #include <stdint.h>
-
 #include "AwFmIndexStruct.h"
 #include "AwFmSimdConfig.h"
 

diff --git a/src/AwFmParallelSearch.c b/src/AwFmParallelSearch.c
@@ -1,11 +1,7 @@
-#include "AwFmParallelSearch.h"
-
 #include <stdbool.h>
 #include <stdint.h>
 #include <stdlib.h>
 #include <string.h>
-
-#include "AwFmFile.h"
 #include "AwFmIndex.h"
 #include "AwFmIndexStruct.h"
 #include "AwFmKmerTable.h"

diff --git a/src/AwFmSearch.c b/src/AwFmSearch.c
@@ -1,5 +1,4 @@
 #include "AwFmSearch.h"
-
 #include "AwFmLetter.h"
 #include "AwFmOccurrence.h"
 #include "AwFmSuffixArray.h"

diff --git a/src/AwFmSearch.h b/src/AwFmSearch.h
@@ -3,7 +3,6 @@
 
 #include <stdbool.h>
 #include <stdint.h>
-
 #include "AwFmFile.h"
 #include "AwFmIndex.h"
 #include "AwFmIndexStruct.h"

diff --git a/src/AwFmSimdConfig.c b/src/AwFmSimdConfig.c
@@ -1,5 +1,4 @@
 #include "AwFmSimdConfig.h"
-
 #include "AwFmIndex.h"
 
 // function implementations are defined based on if they're ARM_NEON (aarch64)

diff --git a/src/AwFmSimdConfig.h b/src/AwFmSimdConfig.h
@@ -2,7 +2,6 @@
 #define AWFM_SIMD_CONFIG_H
 
 #include <stdint.h>
-
 #include "AwFmIndex.h"
 
 /*

diff --git a/src/AwFmSuffixArray.c b/src/AwFmSuffixArray.c
@@ -2,7 +2,6 @@
 
 #include <assert.h>
 #include <string.h>
-
 #include "AwFmFile.h"
 
 // adding padding bytes prevents buffer overflow problems recalling values from

diff --git a/test/backtraceTest/backtraceTest.c b/test/backtraceTest/backtraceTest.c
@@ -1,12 +1,6 @@
 #include "../../build/FastaVector.h"
 #include "../../build/divsufsort64.h"
-#include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
-#include "../../src/AwFmIndexStruct.h"
-#include "../../src/AwFmKmerTable.h"
-#include "../../src/AwFmLetter.h"
-#include "../../src/AwFmOccurrence.h"
-#include "../../src/AwFmParallelSearch.h"
 #include "../../src/AwFmSearch.h"
 #include "../test.h"
 #include <assert.h>

diff --git a/test/bwtTest/bwtTest.c b/test/bwtTest/bwtTest.c
@@ -1,5 +1,4 @@
 #include <assert.h>
-#include <ctype.h>
 #include <stdbool.h>
 #include <stdint.h>
 #include <stdio.h>
@@ -8,10 +7,7 @@
 #include <time.h>
 
 #include "../../build/divsufsort64.h"
-#include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
-#include "../../src/AwFmIndexStruct.h"
-#include "../../src/AwFmKmerTable.h"
 #include "../../src/AwFmLetter.h"
 #include "../../src/AwFmOccurrence.h"
 #include "../test.h"

diff --git a/test/createTests/AwFmCreationTest.c b/test/createTests/AwFmCreationTest.c
@@ -1,5 +1,4 @@
 #include <assert.h>
-#include <ctype.h>
 #include <stdbool.h>
 #include <stdint.h>
 #include <stdio.h>
@@ -8,7 +7,6 @@
 #include <time.h>
 
 #include "../../build/divsufsort64.h"
-#include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
 #include "../../src/AwFmIndexStruct.h"
 #include "../../src/AwFmKmerTable.h"

diff --git a/test/fileTests/AwFmFileTests.c b/test/fileTests/AwFmFileTests.c
@@ -7,14 +7,8 @@
 #include <time.h>
 
 #include "../../build/divsufsort64.h"
-#include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
 #include "../../src/AwFmIndexStruct.h"
-#include "../../src/AwFmKmerTable.h"
-#include "../../src/AwFmLetter.h"
-#include "../../src/AwFmOccurrence.h"
-#include "../../src/AwFmParallelSearch.h"
-#include "../../src/AwFmSearch.h"
 #include "../../src/AwFmSuffixArray.h"
 #include "../test.h"
 

diff --git a/test/inMemorySaTest/inMemorySaTest.c b/test/inMemorySaTest/inMemorySaTest.c
@@ -7,14 +7,7 @@
 #include <time.h>
 
 #include "../../build/divsufsort64.h"
-#include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
-#include "../../src/AwFmIndexStruct.h"
-#include "../../src/AwFmKmerTable.h"
-#include "../../src/AwFmLetter.h"
-#include "../../src/AwFmOccurrence.h"
-#include "../../src/AwFmParallelSearch.h"
-#include "../../src/AwFmSearch.h"
 #include "../test.h"
 
 char buffer[2048];

diff --git a/test/kmerSeedTableTests/kmerSeedTableTests.c b/test/kmerSeedTableTests/kmerSeedTableTests.c
@@ -1,5 +1,4 @@
 #include <assert.h>
-#include <ctype.h>
 #include <stdbool.h>
 #include <stdint.h>
 #include <stdio.h>
@@ -8,11 +7,9 @@
 #include <time.h>
 
 #include "../../build/divsufsort64.h"
-#include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
 #include "../../src/AwFmIndexStruct.h"
 #include "../../src/AwFmKmerTable.h"
-#include "../../src/AwFmLetter.h"
 #include "../../src/AwFmSearch.h"
 #include "../test.h"
 

diff --git a/test/letterTest/AwFmLetterTest.c b/test/letterTest/AwFmLetterTest.c
@@ -9,7 +9,6 @@
 #include <string.h>
 #include <time.h>
 
-#include "../../src/AwFmIndexStruct.h"
 #include "../test.h"
 
 char buffer[2048];

diff --git a/test/multiSequenceIndexTest/AwFmMultiSequenceTest.c b/test/multiSequenceIndexTest/AwFmMultiSequenceTest.c
@@ -7,13 +7,8 @@
 #include <time.h>
 
 #include "../../lib/FastaVector/src/FastaVector.h"
-#include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
 #include "../../src/AwFmIndexStruct.h"
-#include "../../src/AwFmKmerTable.h"
-#include "../../src/AwFmLetter.h"
-#include "../../src/AwFmOccurrence.h"
-#include "../../src/AwFmParallelSearch.h"
 #include "../../src/AwFmSearch.h"
 #include "../../src/AwFmSuffixArray.h"
 #include "../test.h"

diff --git a/test/occurrenceTests/occurrenceTests.c b/test/occurrenceTests/occurrenceTests.c
@@ -6,13 +6,8 @@
 #include <time.h>
 
 #include "../../build/divsufsort64.h"
-#include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
-#include "../../src/AwFmIndexStruct.h"
-#include "../../src/AwFmKmerTable.h"
 #include "../../src/AwFmLetter.h"
-#include "../../src/AwFmOccurrence.h"
-#include "../../src/AwFmSearch.h"
 #include "../../src/AwFmSimdConfig.h"
 #include "../test.h"
 

diff --git a/test/searchTest/searchTest.c b/test/searchTest/searchTest.c
@@ -7,13 +7,8 @@
 #include <time.h>
 
 #include "../../build/divsufsort64.h"
-#include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
 #include "../../src/AwFmIndexStruct.h"
-#include "../../src/AwFmKmerTable.h"
-#include "../../src/AwFmLetter.h"
-#include "../../src/AwFmOccurrence.h"
-#include "../../src/AwFmSearch.h"
 #include "../test.h"
 
 char buffer[2048];

diff --git a/test/sharedLibTest/awfmiTest.c b/test/sharedLibTest/awfmiTest.c
@@ -2,7 +2,6 @@
 #include <stdint.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <string.h>
 
 int main(int argc, char **argv) {
   struct AwFmIndex *index;

diff --git a/test/staticLibTest/awfmiTest.c b/test/staticLibTest/awfmiTest.c
@@ -2,7 +2,6 @@
 #include <stdint.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <string.h>
 
 int main(int argc, char **argv) {
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,7 +3,6 @@ @@
     #include <stdbool.h>
     #include <stdint.h>
     #include "AwFmIndexStruct.h"
     /*
@@ Expand Down @@