bio-bigwig 0.1.0 → 0.1.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 972d5cd642441b8881267966c288fec25708aba244c7aa8ca2618d0888ca769e
-  data.tar.gz: 328fd1c1d6f0705a8eef2144c1f4894b9f27bc58d35c5e3e20ea15fd58e4e776
+  metadata.gz: b9937e02151804bc5a6440481d7e6ec99ff411e474f04c6889b86d6a396287f5
+  data.tar.gz: ec2cef28451cb57e4cfd3e49436f86e64e248a804032b40e8cff3f4817f9bc98
 SHA512:
-  metadata.gz: 40ede32f219724178e4076ede669ab89f2d68065ff5becf16f84b7e8d6c2b0636d3a3c51bf1d0d3f3a29b37dbacf232a167bccf838882e6d946c35779fa8c075
-  data.tar.gz: 608f3bf25e5b549ad6c31d7bf41f6a8d7b55f735721ccf19a33843390e6038bd1b0fbdc28693c9321101de9aa54495952e2565700fe38bc30097e8e7d979f6e3
+  metadata.gz: c3110386fbb9c9c9b892a934abc6ac5f66b10049e4c6a69cd23727a2e7a83ac111a6801122e1c49619e5b905ef06a87c27a5c1696111a6c7121e5c5afd0b4013
+  data.tar.gz: c77e2b59ab87c285b111f46d466f8e71272355666ac3940253675536e58f1c0a4cbc3d2ed6a971558c53b4e1201c2a0340ff75b842335f176722ff6dfe023402

data/ext/bio/bigwig/extconf.rb

@@ -2,6 +2,7 @@ require "mkmf"
 
 # check curl
 have_library("curl", "curl_easy_init")
+have_library("z", "uncompress", "zlib.h")
 have_header("libbigwig/bigWig.h")
 
 $srcs = Dir.glob("libBigWig/*.c", base: __dir__)

data/ext/bio/bigwig/libBigWig/bigWig.h

@@ -56,7 +56,7 @@ extern "C" {
 /*!
  * The library version number
  */
-#define LIBBIGWIG_VERSION 0.4.8
+#define LIBBIGWIG_VERSION 0.4.10
 
 /*!
  * If 1, then this library was compiled with remote file support.

data/ext/bio/bigwig/libBigWig/bwValues.c

@@ -487,7 +487,7 @@ bbOverlappingEntries_t *bbGetOverlappingEntriesCore(bigWigFile_t *fp, bwOverlapB
     uint64_t i;
     int compressed = 0, rv, slen;
     uLongf sz = fp->hdr->bufSize, tmp = 0;
-    void *buf = NULL, *bufEnd = NULL, *compBuf = NULL;
+    void *buf = NULL, *bufBase = NULL, *bufEnd = NULL, *compBuf = NULL;
     uint32_t entryTid = 0, start = 0, end;
     char *str;
     bbOverlappingEntries_t *output = calloc(1, sizeof(bbOverlappingEntries_t));
@@ -499,7 +499,7 @@ bbOverlappingEntries_t *bbGetOverlappingEntriesCore(bigWigFile_t *fp, bwOverlapB
 
     if(sz) {
         compressed = 1;
-        buf = malloc(sz);
+        bufBase = buf = malloc(sz);
     }
     sz = 0; //This is now the size of the compressed buffer
 
@@ -544,15 +544,14 @@ bbOverlappingEntries_t *bbGetOverlappingEntriesCore(bigWigFile_t *fp, bwOverlapB
         buf = (char*)bufEnd - tmp; //reset the buffer pointer
     }
 
-    if(compressed && buf) free(buf);
+    if(compressed && bufBase) free(bufBase);
     if(compBuf) free(compBuf);
     return output;
 
 error:
     fprintf(stderr, "[bbGetOverlappingEntriesCore] Got an error\n");
-    buf = (char*)bufEnd - tmp;
     if(output) bbDestroyOverlappingEntries(output);
-    if(compressed && buf) free(buf);
+    if(compressed && bufBase) free(bufBase);
     if(compBuf) free(compBuf);
     return NULL;
 }

data/ext/bio/bigwig/libBigWig/bwWrite.c

@@ -544,7 +544,7 @@ int bwAddIntervalSpanSteps(bigWigFile_t *fp, const char *chrom, uint32_t start,
         updateStats(fp, wb->span, values[i]);
         wb->l += 4;
     }
-    wb->end = wb->start + (wb->l>>2) * step;
+    wb->end = wb->start + ((wb->l-24)>>2) * step;
 
     return 0;
 }
@@ -567,7 +567,7 @@ int bwAppendIntervalSpanSteps(bigWigFile_t *fp, const float *values, uint32_t n)
         updateStats(fp, wb->span, values[i]);
         wb->l += 4;
     }
-    wb->end = wb->start + (wb->l>>2) * wb->step;
+    wb->end = wb->start + ((wb->l-24)>>2) * wb->step;
 
     return 0;
 }

data/ext/bio/bigwig/libBigWig/io.c

@@ -209,6 +209,11 @@ URL_t *urlOpen(const char *fname, CURLcode (*callBack)(CURL*), const char *mode)
                 fprintf(stderr, "[urlOpen] Failed instructing curl to use any HTTP authentication it finds to be suitable!\n");
                 goto error;
             }
+            // set user-agent
+            if(curl_easy_setopt(URL->x.curl, CURLOPT_USERAGENT, "libBigWig") != CURLE_OK) {
+                fprintf(stderr, "[urlOpen] Failed instructing curl to use libBigWig as a user-agent!\n");
+                goto error;
+            }
             //Follow redirects
             if(curl_easy_setopt(URL->x.curl, CURLOPT_FOLLOWLOCATION, 1L) != CURLE_OK) {
                 fprintf(stderr, "[urlOpen] Failed instructing curl to follow redirects!\n");

data/lib/bio/bigwig/version.rb

@@ -2,6 +2,6 @@
 
 module Bio
   class BigWig
-    VERSION = "0.1.0"
+    VERSION = "0.1.2"
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-bigwig
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.2
 platform: ruby
 authors:
 - kojix2
@@ -53,7 +53,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.6.9
+rubygems_version: 4.0.20
 specification_version: 4
 summary: A ruby library for accessing bigWig / bigBed files
 test_files: []