bio-bigwig 0.0.2 → 0.0.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: f41aa1f4b018bb4e095d971cff0aa56e82ff4e0e9b1be3f542c2479c10d5a8da
-  data.tar.gz: 84de77c8c84d1542e14b34066f26fd969bb009dd94c7f6e9ed52a9b37d01a849
+  metadata.gz: 9fc197bd8ffd3edcbecd7c74e632b9b44d180b30540194e083aa23245822322d
+  data.tar.gz: 52075f2eccf948d9017e4b94ba5b4380cd66729610f8fbabe1a16732649ec5f6
 SHA512:
-  metadata.gz: 940906811fbe9f4500e8ffaeaee6828482e90ecf2d4842bcc3b7521c5a3202b09c6e05e06448dbabc798ee45a148de0a6264a2a3b5deae4a00976684b6807b64
-  data.tar.gz: cf77bebe39c40252a9aa0c6f62b2457bb143c380128fc5dae75f6628a0109fb93336d005c3e4e1d30cec716f8ed152e25324eb5f849e5fdcc402390a5f9346c6
+  metadata.gz: 27b8667fabdc77ef6e66544af79ccf9c2ea67c7a661649f7add0590f739ed82b0cc57026a6ffd23c7923faa1d9154146213d51fd6f2b56d6f43681b7f6fb00fb
+  data.tar.gz: 7a580a0ef61afdbcdb6eb56507de67c6a91bc610558e36892fae6ebca7b049aaec749012488613e40890a88d25d3c7370e467cbf691b47dca389caf278a69294

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));
@@ -498,7 +498,7 @@ 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 +522,7 @@ 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)
   {
@@ -589,7 +589,7 @@ 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 +641,8 @@ 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;
 }
@@ -696,11 +697,17 @@ 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_eRuntimeError, "The bigWig file handle is not opened!");
+    return Qnil;
+  }
+
+  if (bw->type == type_check)
   {
     return Qtrue;
   }
@@ -711,18 +718,15 @@ 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()

data/ext/bio/bigwig/libBigWig/LICENSE

@@ -0,0 +1,22 @@
+The MIT License (MIT)
+
+Copyright (c) 2015 Devon Ryan
+
+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.
+