Fix #24, properly handle 32-bit files

Author: Devon Ryan

lib2bit/2bit.c

@@ -212,7 +212,7 @@ char *twobitSequence(TwoBit *tb, char *chrom, uint32_t start, uint32_t end) {
             break;
         }
     }
-    if(tid == 0 && strcmp(tb->cl->chrom[i], chrom) != 0) return NULL;
+    if(tid == 0 && strcmp(tb->cl->chrom[tid], chrom) != 0) return NULL;
 
     //Get the start/end if not specified
     if(start == end && end == 0) {
@@ -406,7 +406,7 @@ void *twobitBases(TwoBit *tb, char *chrom, uint32_t start, uint32_t end, int fra
         }
     }
 
-    if(tid == 0 && strcmp(tb->cl->chrom[i], chrom) != 0) return NULL;
+    if(tid == 0 && strcmp(tb->cl->chrom[tid], chrom) != 0) return NULL;
 
     //Get the start/end if not specified
     if(start == end && end == 0) {
@@ -517,7 +517,7 @@ void twobitIndexRead(TwoBit *tb, int storeMasked) {
             for(i=0; i<tb->hdr->nChroms; i++) {
                 if(idx->nBlockSizes[i]) free(idx->nBlockSizes[i]);
             }
-            free(idx->nBlockSizes[i]);
+            free(idx->nBlockSizes);
         }
 
         if(idx->maskBlockCount) free(idx->maskBlockCount);
@@ -587,13 +587,15 @@ void twobitChromListRead(TwoBit *tb) {
     TwoBitCL *cl = calloc(1, sizeof(TwoBitCL));
     uint8_t useLong = tb->hdr->version == 1;
     size_t offsetSz = (useLong) ? sizeof(uint64_t) : sizeof(uint32_t);
+    void *offset = calloc(1, offsetSz);
 
     //Allocate cl and do error checking
     if(!cl) goto error;
     cl->chrom = calloc(tb->hdr->nChroms, sizeof(char*));
-    cl->offset = calloc(tb->hdr->nChroms, offsetSz);
+    cl->offset = calloc(tb->hdr->nChroms, sizeof(uint64_t));
     if(!cl->chrom) goto error;
     if(!cl->offset) goto error;
+    if(!offset) goto error;
 
     for(i=0; i<tb->hdr->nChroms; i++) {
         //Get the string size (not null terminated!)
@@ -607,8 +609,14 @@ void twobitChromListRead(TwoBit *tb) {
         str = NULL;
 
         //Read in the size
-        if(twobitRead(cl->offset + i, offsetSz, 1, tb) != 1) goto error;
+        if(twobitRead(offset, offsetSz, 1, tb) != 1) goto error;
+        if(useLong) {
+            cl->offset[i] = *((uint64_t*) offset);
+        } else {
+            cl->offset[i] = *((uint32_t*) offset);
+        }
     }
+    free(offset);
 
     tb->cl = cl;
     return;
@@ -625,6 +633,7 @@ void twobitChromListRead(TwoBit *tb) {
         }
         free(cl);
     }
+    if(offset) free(offset);
 }
 
 void twobitChromListDestroy(TwoBit *tb) {

py2bit.h

@@ -1,7 +1,7 @@
 #include <Python.h>
 #include "2bit.h"
 
-#define pyTwoBitVersion "1.0.0"
+#define pyTwoBitVersion "1.0.1"
 
 typedef struct {
     PyObject_HEAD

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "py2bit"
-version = "1.0.0"
+version = "1.0.1"
 description = "A package for accessing 2bit files using lib2bit"
 authors = [
     { name = "Devon P. Ryan", email = "dpryan79@gmail.com" }