Merge pull request #5 from dpryan79/fix4

Fix #4

Author: dpryan79

lib2bit/2bit.c

@@ -72,6 +72,7 @@ void bytes2bases(char *seq, uint8_t *byte, uint32_t sz, int offset) {
         while(offset < 4) {
            seq[pos++] = byte2base(foo, offset++);
         }
+        if(pos >= sz) return;
         foo = byte[++i];
     }
 
@@ -158,9 +159,10 @@ void softMask(char *seq, TwoBit *tb, uint32_t tid, uint32_t start, uint32_t end)
 */
 char *constructSequence(TwoBit *tb, uint32_t tid, uint32_t start, uint32_t end) {
     uint32_t sz = end - start + 1;
-    uint32_t blockStart, blockEnd, offset;
+    uint32_t blockStart, blockEnd;
     char *seq = malloc(sz * sizeof(char));
     uint8_t *bytes = NULL;
+    int offset;
     if(!seq) return NULL;
 
     //There are 4 bases/byte

py2bitTest/test.py

@@ -41,3 +41,8 @@ def testBases(self):
         assert(tb.bases("chr1", 24, 74) == {'A': 0.12, 'C': 0.12, 'T': 0.12, 'G': 0.12})
         assert(tb.bases("chr1", 24, 74, False) == {'A': 6, 'C': 6, 'T': 6, 'G': 6})
         tb.close()
+
+    def testSequence(self):
+        tb = py2bit.open(self.fname, True)
+        assert(tb.sequence("chr1", 1, 3) == "NN")
+        assert(tb.sequence("chr1", 1, 2) == "N")

setup.py

@@ -17,13 +17,13 @@
                     include_dirs = ['lib2bit', sysconfig.get_config_var("INCLUDEPY")])
 
 setup(name = 'py2bit',
-       version = '0.2.0',
+       version = '0.2.1',
        description = 'A package for accessing 2bit files using lib2bit',
        author = "Devon P. Ryan",
        author_email = "ryan@ie-freiburg.mpg.de",
        url = "https://github.com/dpryan79/py2bit",
        license = "MIT",
-       download_url = "https://github.com/dpryan79/py2bit/tarball/0.2.0",
+       download_url = "https://github.com/dpryan79/py2bit/tarball/0.2.1",
        keywords = ["bioinformatics", "2bit"],
        classifier = ["Development Status :: 5 - Production/Stable",
                      "Intended Audience :: Developers",