Merge pull request #28 from dpryan79/libBigWig-0.3.1

Copy over libBigWig 0.3.1 and bump pyBigWig version to 0.3.3

Author: dpryan79

libBigWig/bigWig.h

@@ -53,7 +53,7 @@ extern "C" {
 /*!
  * The library version number
  */
-#define LIBBIGWIG_VERSION 0.3.0
+#define LIBBIGWIG_VERSION 0.3.1
 
 /*!
  * The magic number of a bigWig file.

libBigWig/bwWrite.c

@@ -780,7 +780,7 @@ int writeIndex(bigWigFile_t *fp) {
 //This may or may not produce the requested number of zoom levels
 int makeZoomLevels(bigWigFile_t *fp) {
     uint32_t meanBinSize, i;
-    uint32_t multiplier = 4, zoom = 10;
+    uint32_t multiplier = 4, zoom = 10, maxZoom = 0;
     uint16_t nLevels = 0;
 
     meanBinSize = ((double) fp->writeBuffer->runningWidthSum)/(fp->writeBuffer->nEntries);
@@ -801,7 +801,15 @@ int makeZoomLevels(bigWigFile_t *fp) {
     if(!fp->hdr->zoomHdrs->indexOffset) return 4;
     if(!fp->hdr->zoomHdrs->idx) return 5;
 
+    //There's no point in having a zoom level larger than the largest chromosome
+    //This will none the less allow at least one zoom level, which is generally needed for IGV et al.
+    for(i=0; i<fp->cl->nKeys; i++) {
+        if(fp->cl->len[i] > maxZoom) maxZoom = fp->cl->len[i];
+    }
+    if(zoom > maxZoom) zoom = maxZoom;
+
     for(i=0; i<fp->hdr->nLevels; i++) {
+        if(zoom > maxZoom) break; //prevent absurdly large zoom levels
         fp->hdr->zoomHdrs->level[i] = zoom;
         nLevels++;
         if(((uint32_t)-1)/multiplier < zoom) break;
@@ -887,6 +895,10 @@ uint32_t updateInterval(bigWigFile_t *fp, bwZoomBuffer_t *buffer, double *sum, d
     uint32_t rv = 0, offset = 0;
     if(!buffer) return 0;
     if(buffer->l+32 >= buffer->m) return 0;
+
+    //Make sure that we don't overflow a uint32_t by adding some huge value to start
+    if(start + size < start) size = ((uint32_t) -1) - start;
+
     if(buffer->l) {
         offset = buffer->l/32;
     } else {

setup.py

@@ -56,12 +56,12 @@
                     include_dirs = include_dirs)
 
 setup(name = 'pyBigWig',
-       version = '0.3.2',
+       version = '0.3.3',
        description = 'A package for accessing bigWig files using libBigWig',
        author = "Devon P. Ryan",
        author_email = "[email protected]",
        url = "https://github.com/dpryan79/pyBigWig",
-       download_url = "https://github.com/dpryan79/pyBigWig/tarball/0.3.2",
+       download_url = "https://github.com/dpryan79/pyBigWig/tarball/0.3.3",
        keywords = ["bioinformatics", "bigWig", "bigBed"],
        classifier = ["Development Status :: 5 - Production/Stable",
                      "Intended Audience :: Developers",