bio-cgranges 0.0.2 → 0.0.4

checksums.yaml

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

@@ -4,6 +4,7 @@
 [![test](https://github.com/kojix2/bio-cgranges/actions/workflows/ci.yml/badge.svg)](https://github.com/kojix2/bio-cgranges/actions/workflows/ci.yml)
 [![docs](https://img.shields.io/badge/docs-stable-blue.svg)](https://rubydoc.info/gems/bio-cgranges)
 [![docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://kojix2.github.io/bio-cgranges/)
+[![DOI](https://zenodo.org/badge/491354623.svg)](https://zenodo.org/badge/latestdoi/491354623)
 
 Ruby bindings to [lh3/cgranges](https://github.com/lh3/cgranges).
 
@@ -71,7 +72,7 @@ bundle exec rake compile
 bundle exec rake test
 ```
 
-Bug reports and pull requests are welcome on GitHub at https://github.com/kojix2/bio-cgranges.
+Bug reports and pull requests are welcome on GitHub at <https://github.com/kojix2/bio-cgranges>.
 
     Do you need commit rights to this repository?
     Do you want to get admin rights and take over the project?

data/ext/bio/cgranges/cgranges/README.md

@@ -122,6 +122,12 @@ for (size_t i = 0; i < a.size(); ++i)
 	printf("%d\t%d\t%d\n", tree.start(a[i]), tree.end(a[i]), tree.data(a[i]));
 ```
 
+## Cite cgranges
+
+This library is integrated into [bedtk][bedtk], which is published in:
+> Li H and Rong J (2021) Bedtk: finding interval overlap with implicit interval tree.
+> *Bioinformatics*, **37**:1315-1316
+
 [bedcov]: https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html
 [ekg-itree]: https://github.com/ekg/intervaltree
 [quicksect]: https://github.com/brentp/quicksect
@@ -131,3 +137,4 @@ for (size_t i = 0; i < a.size(); ++i)
 [bheap]: https://en.wikipedia.org/wiki/Binary_heap
 [ailist]: https://www.biorxiv.org/content/10.1101/593657v1
 [kerneltree]: https://github.com/biocore-ntnu/kerneltree
+[bedtk]: https://github.com/lh3/bedtk

data/ext/bio/cgranges/cgranges.c

@@ -75,7 +75,7 @@ cgranges_memsize(const void *ptr)
   return data ? sizeof(*data) : 0;
 }
 
-static cgranges_t *get_cganges(VALUE self)
+static cgranges_t *get_cgranges(VALUE self)
 {
   cgranges_t *ptr = NULL;
   TypedData_Get_Struct(self, cgranges_t, &cgranges_type, ptr);
@@ -120,7 +120,7 @@ cgranges_init(VALUE self)
 static VALUE
 cgranges_add(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en, VALUE rb_label)
 {
-  cgranges_t *cr = get_cganges(self);
+  cgranges_t *cr = get_cgranges(self);
   cr_intv_t *intv = NULL;
   char *ctg = NULL;
   int32_t st = 0;
@@ -162,7 +162,7 @@ cgranges_index(VALUE self)
     return Qnil;
   }
 
-  cgranges_t *cr = get_cganges(self);
+  cgranges_t *cr = get_cgranges(self);
   cr_index(cr);
 
   rb_ivar_set(self, rb_intern("@indexed"), Qtrue);
@@ -180,7 +180,7 @@ cgranges_index(VALUE self)
 static VALUE
 cgranges_overlap(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
 {
-  cgranges_t *cr = get_cganges(self);
+  cgranges_t *cr = get_cgranges(self);
   char *ctg = NULL;
   int32_t st = 0;
   int32_t en = 0;
@@ -203,6 +203,7 @@ cgranges_overlap(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
 
   if (n < 0)
   {
+    free(b);
     rb_raise(rb_eRuntimeError, "Error finding overlaps");
     return Qnil;
   }
@@ -230,7 +231,7 @@ cgranges_overlap(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
 static VALUE
 cgranges_count_overlap(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
 {
-  cgranges_t *cr = get_cganges(self);
+  cgranges_t *cr = get_cgranges(self);
   char *ctg = NULL;
   int32_t st = 0;
   int32_t en = 0;
@@ -253,6 +254,7 @@ cgranges_count_overlap(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
 
   if (n < 0)
   {
+    free(b);
     rb_raise(rb_eRuntimeError, "Error finding overlaps");
     return Qnil;
   }
@@ -271,7 +273,7 @@ cgranges_count_overlap(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
 static VALUE
 cgranges_contain(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
 {
-  cgranges_t *cr = get_cganges(self);
+  cgranges_t *cr = get_cgranges(self);
   char *ctg = NULL;
   int32_t st = 0;
   int32_t en = 0;
@@ -294,6 +296,7 @@ cgranges_contain(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
 
   if (n < 0)
   {
+    free(b);
     rb_raise(rb_eRuntimeError, "Error finding contained");
     return Qnil;
   }
@@ -321,7 +324,7 @@ cgranges_contain(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
 static VALUE
 cgranges_count_contain(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
 {
-  cgranges_t *cr = get_cganges(self);
+  cgranges_t *cr = get_cgranges(self);
   char *ctg = NULL;
   int32_t st = 0;
   int32_t en = 0;
@@ -344,6 +347,7 @@ cgranges_count_contain(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
 
   if (n < 0)
   {
+    free(b);
     rb_raise(rb_eRuntimeError, "Error finding contained");
     return Qnil;
   }
@@ -355,7 +359,7 @@ cgranges_count_contain(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
 static VALUE
 cgranges_coverage(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en, int contain)
 {
-  cgranges_t *cr = get_cganges(self);
+  cgranges_t *cr = get_cgranges(self);
   char *ctg = NULL;
   int32_t st1 = 0;
   int32_t en1 = 0;
@@ -386,6 +390,7 @@ cgranges_coverage(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en, int contai
 
   if (n < 0)
   {
+    free(b);
     rb_raise(rb_eRuntimeError, "Error finding overlaps");
     return Qnil;
   }

data/lib/bio/cgranges/version.rb

@@ -2,6 +2,6 @@
 
 module Bio
   class CGRanges
-    VERSION = "0.0.2"
+    VERSION = "0.0.4"
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-cgranges
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.4
 platform: ruby
 authors:
 - kojix2
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-11-03 00:00:00.000000000 Z
+date: 2024-09-19 00:00:00.000000000 Z
 dependencies: []
 description: Genomic interval overlap queries
 email:
@@ -35,7 +35,7 @@ homepage: https://github.com/kojix2/bio-cgranges
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -50,8 +50,8 @@ 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 bindings for lh3/cgranges
 test_files: []