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EBI-Metagenomics · Dec 1, 2023 · 7cd4b5b · 7cd4b5b
1 parent d34ff33
commit 7cd4b5b
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Showing 67 changed files with 129 additions and 213 deletions.
diff --git a/c-core/argmax.h b/c-core/argmax.h
diff --git a/c-core/argmax_avx.h b/c-core/argmax_avx.h
@@ -1,10 +1,11 @@
 #ifndef ARGMAX_AVX_H
 #define ARGMAX_AVX_H
 
+#if __AVX__
 #include "argmax_generic.h"
 #include "compiler.h"
-#include "find.h"
-#include "vmax.h"
+#include "find_avx.h"
+#include "vmax_avx.h"
 
 PURE int argmax2(float *dval, float const x[restrict])
 {
@@ -42,5 +43,6 @@ PURE int argmax20(float *dval, float const x[restrict])
   *dval = val;
   return i;
 }
+#endif
 
 #endif
diff --git a/c-core/argmax_neon.h b/c-core/argmax_neon.h
@@ -1,10 +1,11 @@
 #ifndef ARGMAX_NEON_H
 #define ARGMAX_NEON_H
 
+#if __ARM_NEON
 #include "argmax_generic.h"
 #include "compiler.h"
-#include "find.h"
-#include "vmax.h"
+#include "find_neon.h"
+#include "vmax_neon.h"
 
 PURE int argmax2(float *dval, float const x[restrict])
 {
@@ -42,5 +43,6 @@ PURE int argmax20(float *dval, float const x[restrict])
   *dval = val;
   return i;
 }
+#endif
 
 #endif
diff --git a/c-core/codec.c b/c-core/codec.c
@@ -1,5 +1,5 @@
 #include "codec.h"
-#include "imm/imm.h"
+#include "imm/path.h"
 #include "protein.h"
 #include "state.h"
 

diff --git a/c-core/database_reader.c b/c-core/database_reader.c
@@ -3,6 +3,9 @@
 #include "defer_return.h"
 #include "error.h"
 #include "lip/1darray/1darray.h"
+#include "lip/file/read_bool.h"
+#include "lip/file/read_float.h"
+#include "lip/file/read_int.h"
 #include "magic_number.h"
 #include "rc.h"
 #include "unpack.h"

diff --git a/c-core/database_reader.h b/c-core/database_reader.h
@@ -2,9 +2,13 @@
 #define DATABASE_READER_H
 
 #include "entry_dist.h"
-#include "imm/imm.h"
-#include "lip/lip.h"
+#include "imm/amino.h"
+#include "imm/nuclt.h"
+#include "imm/nuclt_code.h"
+#include "lip/file/file.h"
 #include "model_params.h"
+#include <stdint.h>
+#include <stdio.h>
 
 struct database_reader
 {

diff --git a/c-core/database_writer.c b/c-core/database_writer.c
@@ -4,6 +4,11 @@
 #include "error.h"
 #include "fs.h"
 #include "lip/1darray/1darray.h"
+#include "lip/file/read_int.h"
+#include "lip/file/write_array.h"
+#include "lip/file/write_bool.h"
+#include "lip/file/write_float.h"
+#include "lip/file/write_int.h"
 #include "magic_number.h"
 #include "pack.h"
 #include "protein.h"

diff --git a/c-core/database_writer.h b/c-core/database_writer.h
@@ -1,8 +1,8 @@
 #ifndef DATABASE_WRITER_H
 #define DATABASE_WRITER_H
 
-#include "imm/imm.h"
-#include "lip/lip.h"
+#include "imm/nuclt_code.h"
+#include "lip/file/file.h"
 #include "model_params.h"
 #include "xlimits.h"
 #include <stdio.h>

diff --git a/c-core/disambiguate.c b/c-core/disambiguate.c
@@ -1,8 +1,6 @@
 #include "array_size.h"
 #include "compiler.h"
-#include <assert.h>
 #include <stddef.h>
-#include <stdio.h>
 
 // clang-format off
 #define ix(x)                                                                  \

diff --git a/c-core/find.h b/c-core/find.h
diff --git a/c-core/find_avx.h b/c-core/find_avx.h
@@ -1,9 +1,9 @@
 #ifndef FIND_AVX_H
 #define FIND_AVX_H
 
+#if __AVX__
 #include "asint.h"
 #include "compiler.h"
-#include "find_generic.h"
 #include <immintrin.h>
 
 PURE int find2(float const needle, float const stack[restrict])
@@ -76,5 +76,6 @@ PURE int find20(float const needle, float const stack[restrict])
   int mask = _mm_movemask_ps(_mm_castsi128_ps(_mm_cmpeq_epi32(zi, ki)));
   return __builtin_ctz(mask << 16);
 }
+#endif
 
 #endif
diff --git a/c-core/find_neon.h b/c-core/find_neon.h
@@ -1,10 +1,9 @@
 #ifndef FIND_NEON_H
 #define FIND_NEON_H
 
+#if __ARM_NEON
 #include "compiler.h"
-#include "find_generic.h"
 #include <arm_neon.h>
-#include <stdio.h>
 
 PURE uint64_t neon_mask64(int32x2_t const needle, float const stack[restrict])
 {
@@ -75,5 +74,6 @@ PURE int find20(float const needle, float const stack[restrict])
   f = neon_mask128(x, stack + 16);
   return (__builtin_ctzll(f) >> 4) + 16;
 }
+#endif
 
 #endif
diff --git a/c-core/fs.c b/c-core/fs.c
@@ -14,15 +14,12 @@
 #endif
 
 #include "fs.h"
-#include "array_size.h"
 #include "error.h"
 #include "rc.h"
 #include "xlimits.h"
 #include "xstrcpy.h"
-#include <assert.h>
 #include <errno.h>
 #include <ftw.h>
-#include <limits.h>
 #include <stdint.h>
 #include <stdlib.h>
 #include <string.h>

diff --git a/c-core/hmm_reader.c b/c-core/hmm_reader.c
@@ -1,8 +1,8 @@
 #include "hmm_reader.h"
-#include "compiler.h"
 #include "error.h"
 #include "model.h"
 #include "rc.h"
+#include <math.h>
 
 static void init_null_lprobs(float[IMM_AMINO_SIZE]);
 

diff --git a/c-core/hmm_reader.h b/c-core/hmm_reader.h
@@ -1,9 +1,7 @@
 #ifndef HMM_READER_H
 #define HMM_READER_H
 
-#include "entry_dist.h"
 #include "hmmer_reader/hmmer_reader.h"
-#include "imm/imm.h"
 #include "model.h"
 #include "model_params.h"
 #include <stdio.h>

diff --git a/c-core/hmmer.c b/c-core/hmmer.c
@@ -1,6 +1,8 @@
 #include "hmmer.h"
 #include "error.h"
-#include "h3client/h3client.h"
+#include "h3client/deadline.h"
+#include "h3client/errno.h"
+#include "h3client/stream.h"
 #include "hmmer_dialer.h"
 #include "hmmer_result.h"
 #include "rc.h"

diff --git a/c-core/hmmer_dialer.c b/c-core/hmmer_dialer.c
@@ -1,6 +1,7 @@
 #include "hmmer_dialer.h"
 #include "error.h"
-#include "h3client/h3client.h"
+#include "h3client/deadline.h"
+#include "h3client/dialer.h"
 #include "hmmer.h"
 #include "rc.h"
 #include <stdlib.h>

diff --git a/c-core/hmmer_result.c b/c-core/hmmer_result.c
@@ -1,6 +1,6 @@
 #include "hmmer_result.h"
 #include "error.h"
-#include "h3client/h3client.h"
+#include "h3client/result.h"
 #include "rc.h"
 #include <math.h>
 #include <stddef.h>

diff --git a/c-core/match.c b/c-core/match.c
@@ -1,7 +1,8 @@
 #include "match.h"
+#include "imm/gencode.h"
+#include "imm/nuclt_code.h"
 #include "protein.h"
 #include "state.h"
-#include <string.h>
 
 struct match match_init(struct protein const *protein)
 {

diff --git a/c-core/match.h b/c-core/match.h
@@ -1,7 +1,8 @@
 #ifndef MATCH_H
 #define MATCH_H
 
-#include "imm/imm.h"
+#include "imm/codon.h"
+#include "imm/step.h"
 #include <stdbool.h>
 
 struct protein;

diff --git a/c-core/match_iter.c b/c-core/match_iter.c
@@ -1,4 +1,5 @@
 #include "match_iter.h"
+#include "imm/path.h"
 #include "match.h"
 
 void match_iter_init(struct match_iter *x, struct imm_seq const *seq,

diff --git a/c-core/model.c b/c-core/model.c
@@ -2,14 +2,20 @@
 #include "defer_return.h"
 #include "entry_dist.h"
 #include "error.h"
-#include "imm/imm.h"
+#include "imm/amino_lprob.h"
+#include "imm/codon_lprob.h"
+#include "imm/gencode.h"
+#include "imm/hmm.h"
+#include "imm/lprob.h"
+#include "imm/nuclt_code.h"
 #include "model.h"
-#include "node.h"
 #include "nuclt_dist.h"
 #include "rc.h"
+#include "state.h"
 #include "xrealloc.h"
 #include <assert.h>
 #include <limits.h>
+#include <math.h>
 #include <stdlib.h>
 #include <string.h>
 

diff --git a/c-core/model.h b/c-core/model.h
@@ -1,14 +1,11 @@
 #ifndef MODEL_H
 #define MODEL_H
 
-#include "entry_dist.h"
-#include "imm/imm.h"
+#include "imm/amino.h"
 #include "model_node.h"
 #include "model_params.h"
 #include "model_xnode.h"
 #include "nuclt_dist.h"
-#include "rc.h"
-#include "state.h"
 #include "trans.h"
 #include "xlimits.h"
 #include "xtrans.h"

diff --git a/c-core/model_node.h b/c-core/model_node.h
@@ -1,7 +1,8 @@
 #ifndef MODEL_NODE_H
 #define MODEL_NODE_H
 
-#include "imm/imm.h"
+#include "imm/frame_state.h"
+#include "imm/mute_state.h"
 #include "nuclt_dist.h"
 
 struct model_node

diff --git a/c-core/model_xnode.h b/c-core/model_xnode.h
@@ -1,7 +1,8 @@
 #ifndef MODEL_XNODE_H
 #define MODEL_XNODE_H
 
-#include "imm/imm.h"
+#include "imm/frame_state.h"
+#include "imm/mute_state.h"
 
 struct model_xnode_null
 {

diff --git a/c-core/nuclt_dist.c b/c-core/nuclt_dist.c
@@ -1,6 +1,7 @@
 #include "nuclt_dist.h"
 #include "error.h"
-#include "lip/lip.h"
+#include "lip/file/read_array.h"
+#include "lip/file/write_array.h"
 #include "rc.h"
 
 void nuclt_dist_init(struct nuclt_dist *x, struct imm_nuclt const *nuclt)

diff --git a/c-core/nuclt_dist.h b/c-core/nuclt_dist.h
@@ -1,7 +1,9 @@
 #ifndef NUCLT_DIST_H
 #define NUCLT_DIST_H
 
-#include "imm/imm.h"
+#include "imm/codon_marg.h"
+#include "imm/nuclt_lprob.h"
+#include <stdio.h>
 
 struct nuclt_dist
 {
@@ -10,6 +12,7 @@ struct nuclt_dist
 };
 
 struct lip_file;
+struct imm_nuclt;
 
 // clang-format off
 void nuclt_dist_init(struct nuclt_dist *, struct imm_nuclt const *);

diff --git a/c-core/pack.h b/c-core/pack.h
@@ -2,9 +2,10 @@
 #define PACK_H
 
 #include "error.h"
-#include "imm/imm.h"
+#include "imm/abc.h"
 #include "lip/1darray/1darray.h"
-#include "lip/lip.h"
+#include "lip/file/write_cstr.h"
+#include "lip/file/write_map.h"
 #include "rc.h"
 
 static inline int pack_key(struct lip_file *stream, char const key[])

diff --git a/c-core/partition_size.c b/c-core/partition_size.c
@@ -1,7 +1,6 @@
 #include "partition_size.h"
-#include "imm/imm.h"
 #include <assert.h>
-#include <limits.h>
+#include "imm/max.h"
 
 static inline long ceildiv(long x, long y)
 {

diff --git a/c-core/press.c b/c-core/press.c
@@ -5,6 +5,7 @@
 #include "error.h"
 #include "fs.h"
 #include "hmm_reader.h"
+#include "imm/gencode.h"
 #include "protein.h"
 #include "rc.h"
 #include "sizeof_field.h"

diff --git a/c-core/product.c b/c-core/product.c
@@ -1,5 +1,4 @@
 #include "product.h"
-#include "array_size.h"
 #include "array_size_field.h"
 #include "defer_return.h"
 #include "error.h"

diff --git a/c-core/product_thread.c b/c-core/product_thread.c
@@ -5,11 +5,9 @@
 #include "format.h"
 #include "fs.h"
 #include "hmmer_result.h"
-#include "imm/imm.h"
 #include "match.h"
 #include "match_iter.h"
 #include "rc.h"
-#include <stdarg.h>
 #include <string.h>
 
 int product_thread_init(struct product_thread *x, int tid, char const *dir)