bio-bigwig 0.0.3 → 0.0.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: '0585eab5aa345929c023943bafc6e27955be406f79379f056a9c45ec5d0b1933'
-  data.tar.gz: 7ffd6b9bcce8e12382fad0fcfe26914f69da45a3db66b022c82007e9820abd9f
+  metadata.gz: 2a7c6f632a8789e179e25df4689ba33ea3afa6ab2e61eaa3eb4e2ec9aa83595b
+  data.tar.gz: d60bff195ccd4b53bce8c7cdc826e204d28df864bf6c564f23dea925e012b751
 SHA512:
-  metadata.gz: 776424b2382940cc1b31242d527b3e468bc5abbfa7a98009fb662389cc79cd2693e49d365423263435db06ab09811d66e5634ca8c07b546ebd46ef1bfb243141
-  data.tar.gz: d245494b5f68359d66fdb80250ab1de08dd9fc21db17f28436e90997b94ca6a5c90f72e9048bcbcf0a4906a274a2785074e57b896def130ab6ebccaa62943881
+  metadata.gz: bf0692a90f5dc3fd04d86f155360d4d917657dfd460fc93f44b49acf8669290d5b9c836b941b7723fdda3ad9afcf7ced19e0e73c5e81ad72df7bd46f8623e674
+  data.tar.gz: 3e9a81e355c12c6c161f46f66a16db12f707135f7b37b9459eb50e4824cf4739759bc346dede7237dafa4d181b0914317de9ccf0e3255df839edf9f2752fa2e3

data/ext/bio/bigwig/bigwigext.c

@@ -89,12 +89,12 @@ bigwig_allocate(VALUE klass)
   return TypedData_Wrap_Struct(klass, &BigWig_type, bw);
 }
 
-//Return 1 if there are any entries at all
+// Return 1 if there are any entries at all
 int hasEntries(bigWigFile_t *bw)
 {
   if (bw->hdr->indexOffset != 0)
     return 1; // No index, no entries pyBigWig issue #111
-  //if(bw->hdr->nBasesCovered > 0) return 1;  // Sometimes headers are broken
+  // if(bw->hdr->nBasesCovered > 0) return 1;  // Sometimes headers are broken
   return 0;
 }
 
@@ -108,7 +108,7 @@ bigwig_init(VALUE self, VALUE rb_fname, VALUE rb_mode)
   fname = StringValueCStr(rb_fname);
   mode = StringValueCStr(rb_mode);
 
-  //Open the local/remote file
+  // Open the local/remote file
   if (strchr(mode, 'w') != NULL || bwIsBigWig(fname, NULL))
   {
     bw = bwOpen(fname, NULL, mode);
@@ -130,7 +130,7 @@ bigwig_init(VALUE self, VALUE rb_fname, VALUE rb_mode)
       goto error;
   }
 
-  //Set the data pointer
+  // Set the data pointer
   DATA_PTR(self) = bw;
 
   rb_ivar_set(self, rb_intern("@last_tid"), INT2NUM(-1));
@@ -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;
   }
 
@@ -397,7 +412,7 @@ 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 +484,7 @@ 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;
   }
 
@@ -498,7 +513,7 @@ bw_get_intervals(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end)
 
   tid = bwGetTid(bw, chrom);
 
-  //Sanity check
+  // Sanity check
   if (endl == (unsigned long)-1 && tid != (uint32_t)-1)
     endl = bw->cl->len[tid];
 
@@ -522,7 +537,7 @@ bw_get_intervals(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end)
     return rb_ary_new2(0);
   }
 
-  //Get the intervals
+  // Get the intervals
   intervals = bwGetOverlappingIntervals(bw, chrom, start, end);
   if (!intervals)
   {
@@ -558,7 +573,7 @@ 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;
   }
 
@@ -589,7 +604,7 @@ bb_get_entries(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end, VALUE r
 
   tid = bwGetTid(bw, chrom);
 
-  //Sanity check
+  // Sanity check
   if (endl == (unsigned long)-1 && tid != (uint32_t)-1)
     endl = bw->cl->len[tid];
   if (tid == (uint32_t)-1 || startl > end || endl > end)
@@ -641,7 +656,8 @@ bb_get_entries(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end, VALUE r
   return ret;
 
 error:
-  bbDestroyOverlappingEntries(o);
+  if (o)
+    bbDestroyOverlappingEntries(o);
   rb_raise(rb_eRuntimeError, "An error occurred while constructing the output!\n");
   return Qnil;
 }
@@ -655,7 +671,7 @@ 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;
   }
 
@@ -683,6 +699,12 @@ 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");
@@ -696,11 +718,17 @@ bw_get_file_type(VALUE self)
 }
 
 static VALUE
-bw_is_bigwig_q(VALUE self)
+bw_is_file_type(VALUE self, int type_check)
 {
   bigWigFile_t *bw = get_bigWigFile(self);
 
-  if (bw->type == 0)
+  if (!bw)
+  {
+    rb_raise(rb_eIOError, "The bigWig file handle is not opened!");
+    return Qnil;
+  }
+
+  if (bw->type == type_check)
   {
     return Qtrue;
   }
@@ -711,18 +739,15 @@ bw_is_bigwig_q(VALUE self)
 }
 
 static VALUE
-bw_is_bigbed_q(VALUE self)
+bw_is_bigwig_q(VALUE self)
 {
-  bigWigFile_t *bw = get_bigWigFile(self);
+  return bw_is_file_type(self, 0); // 0 = BigWig
+}
 
-  if (bw->type == 1)
-  {
-    return Qtrue;
-  }
-  else
-  {
-    return Qfalse;
-  }
+static VALUE
+bw_is_bigbed_q(VALUE self)
+{
+  return bw_is_file_type(self, 1); // 1 = BigBed
 }
 
 void Init_bigwigext()
@@ -734,6 +759,7 @@ 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 = "0.0.3"
+    VERSION = "0.0.5"
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-bigwig
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.5
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-09-20 00:00:00.000000000 Z
+date: 2024-09-24 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.