edlib 0.0.7 → 0.0.9

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -38,6 +38,26 @@ a.align("AACG", "TCAACCTG")
 |task                 |DISTANCE, LOC, PATH ["DISTANCE"]                                                    |
 |additional_equalities|List of pairs of characters, where each pair defines two characters as equal. [NULL]|
 
+
+```ruby
+a.align("AACG", "TCAACCTG", nice: true)
+
+# {
+#   :edit_distance=>1,                                                 
+#   :alphabet_length=>4,                                               
+#   :locations=>[[2, 4], [2, 5]],                                      
+#   :alignment=>[0, 0, 0, 1],                                          
+#   :cigar=>"3=1I",                                                    
+#   :query_aligned=>"AACG",                                            
+#   :match_aligned=>"|||-",                                            
+#   :target_aligned=>"AAC-"
+# }        
+```
+
+## Documentation
+
+https://kojix2.github.io/ruby-edlib/
+
 ## Development
 
 Pull requests welcome!

data/ext/edlib/LICENSE

@@ -0,0 +1,20 @@
+The MIT License (MIT)
+
+Copyright (c) 2014 Martin Šošić
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/ext/edlib/edlib.cpp

@@ -889,10 +889,10 @@ static int myersCalcEditDistanceNW(const Word* const Peq, const int W, const int
                 (*alignData)->Ps[maxNumBlocks * c + b] = bl->P;
                 (*alignData)->Ms[maxNumBlocks * c + b] = bl->M;
                 (*alignData)->scores[maxNumBlocks * c + b] = bl->score;
-                (*alignData)->firstBlocks[c] = firstBlock;
-                (*alignData)->lastBlocks[c] = lastBlock;
                 bl++;
             }
+            (*alignData)->firstBlocks[c] = firstBlock;
+            (*alignData)->lastBlocks[c] = lastBlock;
         }
         //----------------------------------------------------------//
         //---- If this is stop column, save it and finish ----//
@@ -901,9 +901,9 @@ static int myersCalcEditDistanceNW(const Word* const Peq, const int W, const int
                 (*alignData)->Ps[b] = (blocks + b)->P;
                 (*alignData)->Ms[b] = (blocks + b)->M;
                 (*alignData)->scores[b] = (blocks + b)->score;
-                (*alignData)->firstBlocks[0] = firstBlock;
-                (*alignData)->lastBlocks[0] = lastBlock;
             }
+            (*alignData)->firstBlocks[0] = firstBlock;
+            (*alignData)->lastBlocks[0] = lastBlock;
             *bestScore_ = -1;
             *position_ = targetStopPosition;
             delete[] blocks;

data/ext/edlib/edlib.h

@@ -200,7 +200,7 @@ extern "C" {
          * 1 stands for insertion to target.
          * 2 stands for insertion to query.
          * 3 stands for mismatch.
-         * Alignment aligns query to target from begining of query till end of query.
+         * Alignment aligns query to target from beginning of query till end of query.
          * If gaps are not penalized, they are not in alignment.
          * If you do not free whole result object using edlibFreeAlignResult(), do not forget to use free().
          */

data/ext/edlib/edlibext.c

@@ -1,20 +1,20 @@
 #include "ruby.h"
 #include "edlibext.h"
 
-#define ALIGNER_GET_(name) \
-	static VALUE \
-	aligner_get_##name(VALUE self) \
-	{ \
-	    EdlibAlignConfig *config = aligner_get_config(self); \
-		return get_##name(config); \
+#define ALIGNER_GET_(name)                               \
+	static VALUE                                           \
+			aligner_get_##name(VALUE self)                     \
+	{                                                      \
+		EdlibAlignConfig *config = aligner_get_config(self); \
+		return get_##name(config);                           \
 	}
 
-#define ALIGNER_SET_(name) \
-	static VALUE \
-	aligner_set_##name(VALUE self, VALUE value) \
-	{ \
-	    EdlibAlignConfig *config = aligner_get_config(self); \
-		return set_##name(config, value); \
+#define ALIGNER_SET_(name)                               \
+	static VALUE                                           \
+			aligner_set_##name(VALUE self, VALUE value)        \
+	{                                                      \
+		EdlibAlignConfig *config = aligner_get_config(self); \
+		return set_##name(config, value);                    \
 	}
 
 VALUE mEdlib;
@@ -26,12 +26,12 @@ static size_t aligner_config_memsize(const void *ptr);
 static void aligner_config_free(void *ptr);
 
 static const rb_data_type_t config_type = {
-	.wrap_struct_name = "RbAlignConfig",
-	.function = {
-		.dfree = aligner_config_free,
-		.dsize = aligner_config_memsize,
-	},
-	.flags = RUBY_TYPED_FREE_IMMEDIATELY,
+		.wrap_struct_name = "RbAlignConfig",
+		.function = {
+				.dfree = aligner_config_free,
+				.dsize = aligner_config_memsize,
+		},
+		.flags = RUBY_TYPED_FREE_IMMEDIATELY,
 };
 
 static VALUE
@@ -131,8 +131,8 @@ set_mode(EdlibAlignConfig *config, VALUE mode)
 	switch (TYPE(mode))
 	{
 	case T_STRING:;
-	    VALUE mode_str = rb_funcall(mode, rb_intern("upcase"), 0);
-	    char *mode_s = RSTRING_PTR(mode_str);
+		VALUE mode_str = rb_funcall(mode, rb_intern("upcase"), 0);
+		char *mode_s = RSTRING_PTR(mode_str);
 		if (strcmp(mode_s, "NW") == 0)
 		{
 			config->mode = EDLIB_MODE_NW;
@@ -252,7 +252,7 @@ static VALUE
 set_additional_equalities(EdlibAlignConfig *config, EdlibEqualityPair *eqpairs, VALUE equalities)
 {
 	Check_Type(equalities, T_ARRAY);
-	int len = RARRAY_LEN(equalities);
+	size_t len = RARRAY_LEN(equalities);
 	if (len == 0)
 	{
 		if (eqpairs != NULL)
@@ -264,9 +264,25 @@ set_additional_equalities(EdlibAlignConfig *config, EdlibEqualityPair *eqpairs,
 		config->additionalEqualitiesLength = 0;
 		return equalities;
 	}
+
+	// Check if len is too large
+	if (len > SIZE_MAX / sizeof(EdlibEqualityPair))
+	{
+		rb_raise(rb_eArgError, "Requested array is too large");
+	}
+
 	char *first_arr = malloc(len * sizeof(char));
 	char *second_arr = malloc(len * sizeof(char));
-	for (int i = 0; i < len; i++)
+	if (first_arr == NULL || second_arr == NULL)
+	{
+		if (first_arr != NULL)
+			free(first_arr);
+		if (second_arr != NULL)
+			free(second_arr);
+		rb_raise(rb_eNoMemError, "Failed to allocate memory for equality pairs");
+	}
+
+	for (size_t i = 0; i < len; i++)
 	{
 		VALUE pair = rb_ary_entry(equalities, i);
 		Check_Type(pair, T_ARRAY);
@@ -295,7 +311,7 @@ set_additional_equalities(EdlibAlignConfig *config, EdlibEqualityPair *eqpairs,
 
 	eqpairs = (EdlibEqualityPair *)malloc(sizeof(EdlibEqualityPair) * len);
 
-	for (int i = 0; i < len; i++)
+	for (size_t i = 0; i < len; i++)
 	{
 		eqpairs[i].first = first_arr[i];
 		eqpairs[i].second = second_arr[i];
@@ -341,7 +357,7 @@ aligner_initialize_raw(VALUE self, VALUE k, VALUE mode, VALUE task, VALUE additi
 	config->k = NUM2INT(k);
 	set_mode(config, mode);
 	set_task(config, task);
-	
+
 	if (additional_equalities != Qnil)
 	{
 		set_additional_equalities(config, eqpairs, additional_equalities);
@@ -365,11 +381,11 @@ aligner_align(VALUE self, VALUE query, VALUE target)
 	}
 
 	EdlibAlignResult result = edlibAlign(
-		StringValueCStr(query),
-		RSTRING_LEN(query),
-		StringValueCStr(target),
-		RSTRING_LEN(target),
-		*config);
+			StringValueCStr(query),
+			RSTRING_LEN(query),
+			StringValueCStr(target),
+			RSTRING_LEN(target),
+			*config);
 
 	if (result.status != 0)
 	{
@@ -413,6 +429,7 @@ aligner_align(VALUE self, VALUE query, VALUE target)
 
 	char *ccigar = edlibAlignmentToCigar(result.alignment, result.alignmentLength, 1); // EDLIB_CIGAR_EXTENDED
 	cigar = rb_str_new2(ccigar);
+	free(ccigar);
 
 	VALUE hash = rb_hash_new();
 	rb_hash_aset(hash, ID2SYM(rb_intern("edit_distance")), edit_distance);

data/lib/edlib/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Edlib
-  VERSION = '0.0.7'
+  VERSION = '0.0.9'
 end

metadata

@@ -1,17 +1,17 @@
 --- !ruby/object:Gem::Specification
 name: edlib
 version: !ruby/object:Gem::Version
-  version: 0.0.7
+  version: 0.0.9
 platform: ruby
 authors:
 - kojix2
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-11-07 00:00:00.000000000 Z
+date: 2024-09-20 00:00:00.000000000 Z
 dependencies: []
-description: 'Lightweight, super fast C/C++ library for sequence alignment using edit
-  (Levenshtein) distance. '
+description: Lightweight, super fast C/C++ library for sequence alignment using edit
+  (Levenshtein) distance.
 email:
 - 2xijok@gmail.com
 executables: []
@@ -20,6 +20,7 @@ extensions:
 extra_rdoc_files: []
 files:
 - README.md
+- ext/edlib/LICENSE
 - ext/edlib/edlib.cpp
 - ext/edlib/edlib.h
 - ext/edlib/edlibext.c
@@ -31,7 +32,7 @@ homepage: https://github.com/kojix2/ruby-edlib
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -46,8 +47,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.7
-signing_key: 
+rubygems_version: 3.5.16
+signing_key:
 specification_version: 4
 summary: ruby-edlib is a wrapper for edlib.
 test_files: []