bio-bigwig 0.1.0 → 0.1.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 972d5cd642441b8881267966c288fec25708aba244c7aa8ca2618d0888ca769e
-  data.tar.gz: 328fd1c1d6f0705a8eef2144c1f4894b9f27bc58d35c5e3e20ea15fd58e4e776
+  metadata.gz: 95e1d69741807991fdf8d393e063690c1df359641277c61ade57183b4ec275e1
+  data.tar.gz: daa00c09d52d963d4a8ff32c45005c24577ccc82c5f41d5aca014f3e9dd08f66
 SHA512:
-  metadata.gz: 40ede32f219724178e4076ede669ab89f2d68065ff5becf16f84b7e8d6c2b0636d3a3c51bf1d0d3f3a29b37dbacf232a167bccf838882e6d946c35779fa8c075
-  data.tar.gz: 608f3bf25e5b549ad6c31d7bf41f6a8d7b55f735721ccf19a33843390e6038bd1b0fbdc28693c9321101de9aa54495952e2565700fe38bc30097e8e7d979f6e3
+  metadata.gz: 4654fa6ed84c7bcd4ca09e2cb70a9498f5a0591644db7562b88a0c73ab8721ae2ba42ca38180ab2caf85b2717bda33760ab950644c19163dc19e37714e3fb34f
+  data.tar.gz: ad73abfb58f31059059aaa415c9a39e305fe1e25cba82d621576fd7a1080db451ca728f2a913ad0224c94e2662560c8e48c7716e46b7366b67fb3a38f11c8aae

data/ext/bio/bigwig/bigwigext.c

@@ -81,6 +81,29 @@ static bigWigFile_t *get_bigWigFile(VALUE obj)
   return data;
 }
 
+static uint32_t
+coordinate_arg(VALUE value)
+{
+  long long coordinate = NUM2LL(value);
+  if (coordinate < 0 || coordinate > UINT32_MAX)
+    rb_raise(rb_eRangeError, "coordinate must be in 0..4294967295");
+  return (uint32_t)coordinate;
+}
+
+static void
+parse_region(bigWigFile_t *bw, uint32_t tid, VALUE rb_start, VALUE rb_end,
+             uint32_t *start, uint32_t *end)
+{
+  if (tid == UINT32_MAX)
+    rb_raise(rb_eRuntimeError, "Invalid interval bounds!");
+
+  *start = NIL_P(rb_start) ? 0 : coordinate_arg(rb_start);
+  *end = NIL_P(rb_end) || rb_end == INT2FIX(-1) ? bw->cl->len[tid] : coordinate_arg(rb_end);
+
+  if (*end <= *start || *end > bw->cl->len[tid])
+    rb_raise(rb_eRuntimeError, "Invalid interval bounds!");
+}
+
 static VALUE
 bigwig_allocate(VALUE klass)
 {
@@ -287,8 +310,7 @@ bw_get_stats(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end, VALUE rb_
 {
   bigWigFile_t *bw = get_bigWigFile(self);
   double *val;
-  unsigned long startl = 0, endl = -1;
-  uint32_t start, end = -1, tid;
+  uint32_t start, end, tid;
   int nBins = 1, i;
   char *chrom = NULL;
   const char *type = "mean";
@@ -317,12 +339,6 @@ bw_get_stats(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end, VALUE rb_
     chrom = StringValueCStr(rb_chrom);
   }
 
-  if (rb_start != Qnil)
-    startl = NUM2LONG(rb_start);
-
-  if (rb_end != Qnil)
-    endl = NUM2LONG(rb_end);
-
   if (rb_nBins != Qnil)
     nBins = NUM2INT(rb_nBins);
 
@@ -330,24 +346,7 @@ bw_get_stats(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end, VALUE rb_
     type = StringValueCStr(rb_type);
 
   tid = bwGetTid(bw, chrom);
-
-  if (endl == (unsigned long)-1 && tid != (uint32_t)-1)
-    endl = bw->cl->len[tid];
-
-  if (tid == (uint32_t)-1 || startl > end || endl > end)
-  {
-    rb_raise(rb_eRuntimeError, "Invalid interval bounds!");
-    return Qnil;
-  }
-
-  start = (uint32_t)startl;
-  end = (uint32_t)endl;
-
-  if (end <= start || end > bw->cl->len[tid] || start >= end)
-  {
-    rb_raise(rb_eRuntimeError, "Invalid interval bounds!");
-    return Qnil;
-  }
+  parse_region(bw, tid, rb_start, rb_end, &start, &end);
 
   if (char2enum(type) == doesNotExist)
   {
@@ -395,8 +394,7 @@ bw_get_values(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end)
 {
   bigWigFile_t *bw = get_bigWigFile(self);
   int i;
-  uint32_t start, end = -1, tid;
-  unsigned long startl = 0, endl = -1;
+  uint32_t start, end, tid;
   char *chrom = NULL;
   VALUE ret;
   bwOverlappingIntervals_t *o;
@@ -418,30 +416,8 @@ bw_get_values(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end)
     chrom = StringValueCStr(rb_chrom);
   }
 
-  if (rb_start != Qnil)
-    startl = NUM2LONG(rb_start);
-
-  if (rb_end != Qnil)
-    endl = NUM2LONG(rb_end);
-
   tid = bwGetTid(bw, chrom);
-
-  if (endl == (unsigned long)-1 && tid != (uint32_t)-1)
-    endl = bw->cl->len[tid];
-  if (tid == (uint32_t)-1 || startl > end || endl > end)
-  {
-    rb_raise(rb_eRuntimeError, "Invalid interval bounds!");
-    return Qnil;
-  }
-
-  start = (uint32_t)startl;
-  end = (uint32_t)endl;
-
-  if (end <= start || end > bw->cl->len[tid] || start >= end)
-  {
-    rb_raise(rb_eRuntimeError, "Invalid interval bounds!");
-    return Qnil;
-  }
+  parse_region(bw, tid, rb_start, rb_end, &start, &end);
 
   if (!hasEntries(bw))
   {
@@ -467,8 +443,7 @@ static VALUE
 bw_get_intervals(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end)
 {
   bigWigFile_t *bw = get_bigWigFile(self);
-  uint32_t start, end = -1, tid, i;
-  unsigned long startl = 0, endl = -1;
+  uint32_t start, end, tid, i;
   bwOverlappingIntervals_t *intervals = NULL;
   char *chrom = NULL;
   VALUE ret;
@@ -496,32 +471,8 @@ bw_get_intervals(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end)
     chrom = StringValueCStr(rb_chrom);
   }
 
-  if (rb_start != Qnil)
-    startl = NUM2LONG(rb_start);
-
-  if (rb_end != Qnil)
-    endl = NUM2LONG(rb_end);
-
   tid = bwGetTid(bw, chrom);
-
-  // 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)
-  {
-    rb_raise(rb_eRuntimeError, "Invalid interval bounds!");
-    return Qnil;
-  }
-
-  start = (uint32_t)startl;
-  end = (uint32_t)endl;
-
-  if (end <= start || end > bw->cl->len[tid] || start >= end)
-  {
-    rb_raise(rb_eRuntimeError, "Invalid interval bounds!");
-    return Qnil;
-  }
+  parse_region(bw, tid, rb_start, rb_end, &start, &end);
 
   if (!hasEntries(bw))
   {
@@ -555,8 +506,7 @@ static VALUE
 bb_get_entries(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end, VALUE rb_with_string)
 {
   bigWigFile_t *bw = get_bigWigFile(self);
-  uint32_t start, end = -1, tid, i;
-  unsigned long startl = 0, endl = -1;
+  uint32_t start, end, tid, i;
   char *chrom = NULL;
   VALUE ret, t;
   int withString = 1;
@@ -579,12 +529,6 @@ bb_get_entries(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end, VALUE r
     chrom = StringValueCStr(rb_chrom);
   }
 
-  if (rb_start != Qnil)
-    startl = NUM2LONG(rb_start);
-
-  if (rb_end != Qnil)
-    endl = NUM2LONG(rb_end);
-
   if (rb_with_string != Qnil)
   {
     if (RTEST(rb_with_string))
@@ -594,24 +538,7 @@ bb_get_entries(VALUE self, VALUE rb_chrom, VALUE rb_start, VALUE rb_end, VALUE r
   }
 
   tid = bwGetTid(bw, chrom);
-
-  // 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)
-  {
-    rb_raise(rb_eRuntimeError, "Invalid interval bounds!");
-    return Qnil;
-  }
-
-  start = (uint32_t)startl;
-  end = (uint32_t)endl;
-
-  if (end <= start || end > bw->cl->len[tid] || start >= end)
-  {
-    rb_raise(rb_eRuntimeError, "Invalid interval bounds!");
-    return Qnil;
-  }
+  parse_region(bw, tid, rb_start, rb_end, &start, &end);
 
   o = bbGetOverlappingEntries(bw, chrom, start, end, withString);
   if (!o)

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 = "0.1.3"
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-bigwig
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.3
 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: []