Merge pull request #23 from dpryan79/fix20

Fix #20 and #22

bwRead.c

@@ -157,6 +157,9 @@ static void bwHdrRead(bigWigFile_t *bw) {
         if(bwRead((void*) &(bw->hdr->sumSquared), sizeof(uint64_t), 1, bw) != 1) goto error;
     }
 
+    //In case of uncompressed remote files, let the IO functions know to request larger chunks
+    bw->URL->isCompressed = (bw->hdr->bufSize > 0)?1:0;
+
     return;
 
 error:

bwStats.c

@@ -92,6 +92,7 @@ static struct vals_t *getVals(bigWigFile_t *fp, bwOverlapBlock_t *o, int i, uint
         if(rv != Z_OK) goto error;
     } else {
         buf = compBuf;
+        sz = o->size[i];
     }
 
     p = buf;
@@ -123,12 +124,12 @@ static struct vals_t *getVals(bigWigFile_t *fp, bwOverlapBlock_t *o, int i, uint
 
     free(v);
     free(buf);
-    free(compBuf);
+    if(compressed) free(compBuf);
     return vals;
 
 error:
     if(buf) free(buf);
-    if(compBuf) free(compBuf);
+    if(compBuf && compressed) free(compBuf);
     if(v) free(v);
     destroyVals_t(vals);
     return NULL;

io.c

@@ -7,6 +7,7 @@
 #include <unistd.h>
 #include "io.h"
 #include <inttypes.h>
+#include <errno.h>
 
 size_t GLOBAL_DEFAULTBUFFERSIZE;
 
@@ -37,15 +38,17 @@ CURLcode urlFetchData(URL_t *URL, unsigned long bufSize) {
     }
 
     rv = curl_easy_perform(URL->x.curl);
+    errno = 0; //Sometimes curl_easy_perform leaves a random errno remnant
     return rv;
 }
 
 //Read data into a buffer, ideally from a buffer already in memory
 //The loop is likely no longer needed.
 size_t url_fread(void *obuf, size_t obufSize, URL_t *URL) {
-    size_t remaining = obufSize;
+    size_t remaining = obufSize, fetchSize;
     void *p = obuf;
     CURLcode rv;
+
     while(remaining) {
         if(!URL->bufLen) {
             rv = urlFetchData(URL, URL->bufSize);
@@ -59,7 +62,12 @@ size_t url_fread(void *obuf, size_t obufSize, URL_t *URL) {
             p += URL->bufLen - URL->bufPos;
             remaining -= URL->bufLen - URL->bufPos;
             if(remaining) {
-                rv = urlFetchData(URL, (remaining<URL->bufSize)?remaining:URL->bufSize);
+                if(!URL->isCompressed) {
+                    fetchSize = URL->bufSize;
+                } else {
+                    fetchSize = (remaining<URL->bufSize)?remaining:URL->bufSize;
+                }
+                rv = urlFetchData(URL, fetchSize);
                 if(rv != CURLE_OK) {
                     fprintf(stderr, "[url_fread] urlFetchData (B) returned %s\n", curl_easy_strerror(rv));
                     return 0;
@@ -227,6 +235,7 @@ URL_t *urlOpen(char *fname, CURLcode (*callBack)(CURL*), const char *mode) {
                 }
             }
             code = curl_easy_perform(URL->x.curl);
+            errno = 0; //Sometimes curl_easy_perform leaves a random errno remnant
             if(code != CURLE_OK) {
                 fprintf(stderr, "[urlOpen] curl_easy_perform received an error: %s\n", curl_easy_strerror(code));
                 goto error;

io.h

@@ -42,6 +42,7 @@ typedef struct {
     size_t bufSize; /**<The size of the buffer.*/
     size_t bufLen; /**<The actual size of the buffer used.*/
     enum bigWigFile_type_enum type; /**<The connection type*/
+    int isCompressed; /**<1 if the file is compressed, otherwise 0*/
     char *fname; /**<Only needed for remote connections. The original URL/filename requested, since we need to make multiple connections.*/
 } URL_t;