- typo :: gap_lineal => gap_linear

- Unified ends-free and end2end code for termination - Added support for indel, edit, and gap-linear (SW)
smarco · Feb 11, 2022 · e0dcb68 · e0dcb68
1 parent 0b1f66e
commit e0dcb68
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Showing 37 changed files with 923 additions and 275 deletions.
diff --git a/Makefile b/Makefile
@@ -31,7 +31,7 @@ SUBDIRS=alignment \
         edit \
         gap_affine \
         gap_affine2p \
-        gap_lineal \
+        gap_linear \
         system \
         utils \
         wavefront

diff --git a/alignment/cigar.c b/alignment/cigar.c
@@ -136,9 +136,9 @@ int cigar_score_edit(
   }
   return score;
 }
-int cigar_score_gap_lineal(
+int cigar_score_gap_linear(
     cigar_t* const cigar,
-    lineal_penalties_t* const penalties) {
+    linear_penalties_t* const penalties) {
   int score = 0, i;
   for (i=cigar->begin_offset;i<cigar->end_offset;++i) {
     switch (cigar->operations[i]) {

diff --git a/alignment/cigar.h b/alignment/cigar.h
@@ -34,7 +34,7 @@
 
 #include "utils/commons.h"
 #include "system/mm_allocator.h"
-#include "gap_lineal/lineal_penalties.h"
+#include "gap_linear/linear_penalties.h"
 #include "gap_affine/affine_penalties.h"
 #include "gap_affine2p/affine2p_penalties.h"
 
@@ -85,9 +85,9 @@ void cigar_add_mismatches(
  */
 int cigar_score_edit(
     cigar_t* const cigar);
-int cigar_score_gap_lineal(
+int cigar_score_gap_linear(
     cigar_t* const cigar,
-    lineal_penalties_t* const penalties);
+    linear_penalties_t* const penalties);
 int cigar_score_gap_affine(
     cigar_t* const cigar,
     affine_penalties_t* const penalties);

diff --git a/benchmark/Makefile b/benchmark/Makefile
@@ -11,7 +11,7 @@ MODULES=benchmark_check \
         benchmark_edit \
         benchmark_gap_affine \
         benchmark_gap_affine2p \
-        benchmark_gap_lineal \
+        benchmark_gap_linear \
         benchmark_utils
 
 SRCS=$(addsuffix .c, $(MODULES))

diff --git a/benchmark/benchmark_check.c b/benchmark/benchmark_check.c
@@ -32,7 +32,7 @@
 #include "benchmark/benchmark_check.h"
 #include "alignment/score_matrix.h"
 #include "edit/edit_dp.h"
-#include "gap_lineal/nw.h"
+#include "gap_linear/nw.h"
 #include "gap_affine/affine_matrix.h"
 #include "gap_affine/swg.h"
 
@@ -70,7 +70,7 @@ void benchmark_check_alignment_edit(
   score_matrix_free(&score_matrix);
   cigar_free(&cigar);
 }
-void benchmark_check_alignment_gap_lineal(
+void benchmark_check_alignment_gap_linear(
     align_input_t* const align_input,
     cigar_t* const cigar_computed) {
   // Compute correct
@@ -83,13 +83,13 @@ void benchmark_check_alignment_gap_lineal(
       align_input->pattern_length+align_input->text_length,
       align_input->mm_allocator);
   nw_compute(&score_matrix,
-      align_input->check_lineal_penalties,
+      align_input->check_linear_penalties,
       align_input->pattern,align_input->pattern_length,
       align_input->text,align_input->text_length,&cigar);
-  const int score_correct = cigar_score_gap_lineal(
-      &cigar,align_input->check_lineal_penalties);
-  const int score_computed = cigar_score_gap_lineal(
-      cigar_computed,align_input->check_lineal_penalties);
+  const int score_correct = cigar_score_gap_linear(
+      &cigar,align_input->check_linear_penalties);
+  const int score_computed = cigar_score_gap_linear(
+      cigar_computed,align_input->check_linear_penalties);
   // Check alignment
   benchmark_check_alignment_using_solution(
       align_input,cigar_computed,score_computed,
@@ -141,8 +141,8 @@ void benchmark_check_alignment(
       (align_input->debug_flags & ALIGN_DEBUG_CHECK_ALIGNMENT)) {
     if (align_input->debug_flags & ALIGN_DEBUG_CHECK_DISTANCE_METRIC_GAP_AFFINE) {
       benchmark_check_alignment_gap_affine(align_input,cigar_computed);
-    } else if(align_input->debug_flags & ALIGN_DEBUG_CHECK_DISTANCE_METRIC_GAP_LINEAL) {
-      benchmark_check_alignment_gap_lineal(align_input,cigar_computed);
+    } else if(align_input->debug_flags & ALIGN_DEBUG_CHECK_DISTANCE_METRIC_GAP_LINEAR) {
+      benchmark_check_alignment_gap_linear(align_input,cigar_computed);
     } else { // ALIGN_DEBUG_CHECK_DISTANCE_METRIC_EDIT
       benchmark_check_alignment_edit(align_input,cigar_computed);
     }

diff --git a/benchmark/benchmark_gap_lineal.c → benchmark/benchmark_gap_linear.c b/benchmark/benchmark_gap_lineal.c → benchmark/benchmark_gap_linear.c
@@ -26,19 +26,19 @@
  *
  * PROJECT: Wavefront Alignments Algorithms
  * AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
- * DESCRIPTION: Gap-lineal alignment algorithms wrapper
+ * DESCRIPTION: Gap-linear alignment algorithms wrapper
  */
 
-#include "benchmark/benchmark_gap_lineal.h"
+#include "benchmark/benchmark_gap_linear.h"
 #include "benchmark/benchmark_check.h"
-#include "gap_lineal/nw.h"
+#include "gap_linear/nw.h"
 
 /*
  * Benchmark NW
  */
-void benchmark_gap_lineal_nw(
+void benchmark_gap_linear_nw(
     align_input_t* const align_input,
-    lineal_penalties_t* const penalties) {
+    linear_penalties_t* const penalties) {
   // Allocate
   score_matrix_t score_matrix;
   score_matrix_allocate(
@@ -60,7 +60,7 @@ void benchmark_gap_lineal_nw(
   }
   // Output
   if (align_input->output_file) {
-    const int score = cigar_score_gap_lineal(&cigar,penalties);
+    const int score = cigar_score_gap_linear(&cigar,penalties);
     FILE* const output_file = align_input->output_file;
     if (align_input->output_full) {
       benchmark_print_output_full(output_file,align_input,score,&cigar);

diff --git a/benchmark/benchmark_gap_lineal.h → benchmark/benchmark_gap_linear.h b/benchmark/benchmark_gap_lineal.h → benchmark/benchmark_gap_linear.h
@@ -26,20 +26,20 @@
  *
  * PROJECT: Wavefront Alignments Algorithms
  * AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
- * DESCRIPTION: Gap-lineal alignment algorithms wrapper
+ * DESCRIPTION: Gap-linear alignment algorithms wrapper
  */
 
-#ifndef BENCHMARK_GAP_LINEAL_H_
-#define BENCHMARK_GAP_LINEAL_H_
+#ifndef BENCHMARK_GAP_LINEAR_H_
+#define BENCHMARK_GAP_LINEAR_H_
 
-#include "gap_lineal/nw.h"
+#include "gap_linear/nw.h"
 #include "benchmark/benchmark_utils.h"
 
 /*
  * Benchmark NW
  */
-void benchmark_gap_lineal_nw(
+void benchmark_gap_linear_nw(
     align_input_t* const align_input,
-    lineal_penalties_t* const penalties);
+    linear_penalties_t* const penalties);
 
-#endif /* BENCHMARK_GAP_LINEAL_H_ */
+#endif /* BENCHMARK_GAP_LINEAR_H_ */
diff --git a/benchmark/benchmark_utils.c b/benchmark/benchmark_utils.c
@@ -32,7 +32,7 @@
 #include "benchmark/benchmark_utils.h"
 #include "alignment/score_matrix.h"
 #include "edit/edit_dp.h"
-#include "gap_lineal/nw.h"
+#include "gap_linear/nw.h"
 #include "gap_affine/affine_matrix.h"
 #include "gap_affine/swg.h"
 

diff --git a/benchmark/benchmark_utils.h b/benchmark/benchmark_utils.h
@@ -47,7 +47,7 @@
 #define ALIGN_DEBUG_DISPLAY_INFO    0x00000008
 
 #define ALIGN_DEBUG_CHECK_DISTANCE_METRIC_EDIT       0x00000010
-#define ALIGN_DEBUG_CHECK_DISTANCE_METRIC_GAP_LINEAL 0x00000040
+#define ALIGN_DEBUG_CHECK_DISTANCE_METRIC_GAP_LINEAR 0x00000040
 #define ALIGN_DEBUG_CHECK_DISTANCE_METRIC_GAP_AFFINE 0x00000080
 
 /*
@@ -87,7 +87,7 @@ typedef struct {
   profiler_counter_t align_ins;
   // DEBUG
   int debug_flags;
-  lineal_penalties_t* check_lineal_penalties;
+  linear_penalties_t* check_linear_penalties;
   affine_penalties_t* check_affine_penalties;
   int check_bandwidth;
   bool verbose;

diff --git a/gap_lineal/Makefile → gap_linear/Makefile b/gap_lineal/Makefile → gap_linear/Makefile
diff --git a/gap_lineal/lineal_penalties.h → gap_linear/linear_penalties.h b/gap_lineal/lineal_penalties.h → gap_linear/linear_penalties.h
@@ -26,17 +26,17 @@
  *
  * PROJECT: Wavefront Alignments Algorithms
  * AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
- * DESCRIPTION: Gap-lineal penalties
+ * DESCRIPTION: Gap-linear penalties
  */
 
-#ifndef LINEAL_PENALTIES_H_
-#define LINEAL_PENALTIES_H_
+#ifndef LINEAR_PENALTIES_H_
+#define LINEAR_PENALTIES_H_
 
 typedef struct {
   int match;              // (Penalty representation; usually M <= 0)
   int mismatch;           // (Penalty representation; usually X > 0)
   int insertion;          // (Penalty representation; usually I > 0)
   int deletion;           // (Penalty representation; usually D > 0)
-} lineal_penalties_t;
+} linear_penalties_t;
 
-#endif /* LINEAL_PENALTIES_H_ */
+#endif /* LINEAR_PENALTIES_H_ */
diff --git a/gap_lineal/nw.c → gap_linear/nw.c b/gap_lineal/nw.c → gap_linear/nw.c
@@ -27,17 +27,17 @@
  * PROJECT: Wavefront Alignments Algorithms
  * AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
  * DESCRIPTION: Dynamic-programming alignment algorithm for computing
- *   gap-lineal pairwise alignment (Needleman-Wunsch - NW)
+ *   gap-linear pairwise alignment (Needleman-Wunsch - NW)
  */
 
-#include "gap_lineal/nw.h"
+#include "gap_linear/nw.h"
 
 /*
  * NW Traceback
  */
 void nw_traceback(
     score_matrix_t* const score_matrix,
-    lineal_penalties_t* const penalties,
+    linear_penalties_t* const penalties,
     cigar_t* const cigar) {
   // Parameters
   int** const dp = score_matrix->columns;
@@ -67,7 +67,7 @@ void nw_traceback(
 }
 void nw_compute(
     score_matrix_t* const score_matrix,
-    lineal_penalties_t* const penalties,
+    linear_penalties_t* const penalties,
     const char* const pattern,
     const int pattern_length,
     const char* const text,

diff --git a/gap_lineal/nw.h → gap_linear/nw.h b/gap_lineal/nw.h → gap_linear/nw.h
@@ -27,7 +27,7 @@
  * PROJECT: Wavefront Alignments Algorithms
  * AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
  * DESCRIPTION: Dynamic-programming alignment algorithm for computing
- *   gap-lineal pairwise alignment (Needleman-Wunsch - NW)
+ *   gap-linear pairwise alignment (Needleman-Wunsch - NW)
  */
 
 #ifndef NW_H_
@@ -41,7 +41,7 @@
  */
 void nw_compute(
     score_matrix_t* const score_matrix,
-    lineal_penalties_t* const penalties,
+    linear_penalties_t* const penalties,
     const char* const pattern,
     const int pattern_length,
     const char* const text,