bio-bigwig 0.0.4 → 0.0.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 9fc197bd8ffd3edcbecd7c74e632b9b44d180b30540194e083aa23245822322d
-  data.tar.gz: 52075f2eccf948d9017e4b94ba5b4380cd66729610f8fbabe1a16732649ec5f6
+  metadata.gz: 87a8791f8697b0b4cff130d28f370e67770688d6da475f7caf956556c8431332
+  data.tar.gz: 8faebc66db077059394015892d69c3dde78e4eee4eb614f36b2b3377bd88450f
 SHA512:
-  metadata.gz: 27b8667fabdc77ef6e66544af79ccf9c2ea67c7a661649f7add0590f739ed82b0cc57026a6ffd23c7923faa1d9154146213d51fd6f2b56d6f43681b7f6fb00fb
-  data.tar.gz: 7a580a0ef61afdbcdb6eb56507de67c6a91bc610558e36892fae6ebca7b049aaec749012488613e40890a88d25d3c7370e467cbf691b47dca389caf278a69294
+  metadata.gz: 017d2fa8b7b03646961344fad93a97d71e9a3d3620e0ced75002d64fa44f5175a8434249ed668924b67b72df2d43a05986dca836018c8e5c144a03ee4a5fa29a
+  data.tar.gz: 9ca76c76d3803689d7e94cd5d9acbd5bd5e939d94bab7a8a2d3c1f0a13ebd5bd3ee97ea617a16877f8a4673ac2fc3291c9b01d56acfa15e70dd05204ec50f398

data/ext/bio/bigwig/bigwigext.c

@@ -162,6 +162,21 @@ bigwig_close(VALUE self)
   return Qnil;
 }
 
+static VALUE
+bigwig_is_closed(VALUE self)
+{
+  bigWigFile_t *bw = get_bigWigFile(self);
+
+  if (bw)
+  {
+    return Qfalse;
+  }
+  else
+  {
+    return Qtrue;
+  }
+}
+
 static VALUE
 bw_get_header(VALUE self)
 {
@@ -170,7 +185,7 @@ bw_get_header(VALUE self)
 
   if (!bw)
   {
-    rb_raise(rb_eRuntimeError, "The bigWig file handle is not opened!");
+    rb_raise(rb_eIOError, "The bigWig file handle is not opened!");
     return Qnil;
   }
 
@@ -210,7 +225,7 @@ bw_get_chroms(int argc, VALUE *argv, VALUE self)
 
   if (!bw)
   {
-    rb_raise(rb_eRuntimeError, "The bigWig file handle is not opened!");
+    rb_raise(rb_eIOError, "The bigWig file handle is not opened!");
     return Qnil;
   }
 
@@ -284,7 +299,7 @@ bw_get_stats(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end, VALUE rb_
 
   if (!bw)
   {
-    rb_raise(rb_eRuntimeError, "The bigWig file handle is not opened!");
+    rb_raise(rb_eIOError, "The bigWig file handle is not opened!");
     return Qnil;
   }
 
@@ -317,12 +332,6 @@ bw_get_stats(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end, VALUE rb_
   if (rb_type != Qnil)
     type = StringValueCStr(rb_type);
 
-  if (rb_exact != Qnil)
-  {
-    if (RTEST(rb_exact) == 1)
-      endl = startl + nBins - 1;
-  }
-
   tid = bwGetTid(bw, chrom);
 
   if (endl == (unsigned long)-1 && tid != (uint32_t)-1)
@@ -397,7 +406,7 @@ bw_get_values(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end)
 
   if (!bw)
   {
-    rb_raise(rb_eRuntimeError, "The bigWig file handle is not opened!");
+    rb_raise(rb_eIOError, "The bigWig file handle is not opened!");
     return Qnil;
   }
 
@@ -469,7 +478,7 @@ bw_get_intervals(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end)
 
   if (!bw)
   {
-    rb_raise(rb_eRuntimeError, "The bigWig file handle is not opened!");
+    rb_raise(rb_eIOError, "The bigWig file handle is not opened!");
     return Qnil;
   }
 
@@ -558,7 +567,7 @@ bb_get_entries(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end, VALUE r
 
   if (!bw)
   {
-    rb_raise(rb_eRuntimeError, "The bigBed file handle is not opened!");
+    rb_raise(rb_eIOError, "The bigBed file handle is not opened!");
     return Qnil;
   }
 
@@ -656,7 +665,7 @@ bb_get_sql(VALUE self)
 
   if (!bw)
   {
-    rb_raise(rb_eRuntimeError, "The bigBed file handle is not opened!");
+    rb_raise(rb_eIOError, "The bigBed file handle is not opened!");
     return Qnil;
   }
 
@@ -684,6 +693,12 @@ bw_get_file_type(VALUE self)
 {
   bigWigFile_t *bw = get_bigWigFile(self);
 
+  if (!bw)
+  {
+    rb_raise(rb_eIOError, "The bigWig file handle is not opened!");
+    return Qnil;
+  }
+
   if (bw->type == 0)
   {
     return rb_str_new2("BigWig");
@@ -703,7 +718,7 @@ bw_is_file_type(VALUE self, int type_check)
 
   if (!bw)
   {
-    rb_raise(rb_eRuntimeError, "The bigWig file handle is not opened!");
+    rb_raise(rb_eIOError, "The bigWig file handle is not opened!");
     return Qnil;
   }
 
@@ -738,6 +753,7 @@ void Init_bigwigext()
 
   rb_define_private_method(rb_BigWig, "initialize_raw", bigwig_init, 2);
   rb_define_method(rb_BigWig, "close", bigwig_close, 0);
+  rb_define_method(rb_BigWig, "closed?", bigwig_is_closed, 0);
   rb_define_method(rb_BigWig, "header", bw_get_header, 0);
   rb_define_method(rb_BigWig, "chroms", bw_get_chroms, -1);
   rb_define_private_method(rb_BigWig, "stats_raw", bw_get_stats, 6);

data/lib/bio/bigwig/version.rb

@@ -2,6 +2,6 @@
 
 module Bio
   class BigWig
-    VERSION = "0.0.4"
+    VERSION = "0.0.6"
   end
 end

data/lib/bio/bigwig.rb

@@ -40,8 +40,8 @@ module Bio
       intervals_raw(chrom, start, stop)
     end
 
-    def entries(chrom, start = 0, stop = -1, text: true)
-      entries_raw(chrom, start, stop, text)
+    def entries(chrom, start = 0, stop = -1, with_string: true)
+      entries_raw(chrom, start, stop, with_string)
     end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-bigwig
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.0.6
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-09-20 00:00:00.000000000 Z
+date: 2024-09-30 00:00:00.000000000 Z
 dependencies: []
 description: This is a Ruby binding for libBigWig (https://github.com/dpryan79/libBigWig),
   which provides high-speed access to bigWig or bigBed files.