Merge pull request #10 from deeptools/dpryan79-patch-1

Fix #9

Author: dpryan79

.travis.yml

@@ -0,0 +1,36 @@
+pr:
+  autoCancel: true
+
+jobs:
+
+- job: 'Linux'
+  pool:
+    vmImage: 'ubuntu-latest'
+  strategy:
+    matrix:
+      Python36:
+        python.version: '3.6'
+      Python37:
+        python.version: '3.7'
+      Python38:
+        python.version: '3.8'
+      Python39:
+        python.version: '3.9'
+      Python310:
+        python.version: '3.10'
+    maxParallel: 5
+
+  steps:
+  - bash: echo "##vso[task.prependpath]/usr/share/miniconda/bin"
+    displayName: Add conda to PATH
+
+  - bash: conda create -n foo -q --yes -c conda-forge -c bioconda python=$(python.version) libcurl zlib pip nose gcc_linux-64
+    displayName: Installing dependencies
+  - bash: |
+      source activate foo
+      python -m pip install . --no-deps --ignore-installed -vvv
+    displayName: Installing py2bit
+  - bash: |
+      source activate foo
+      nosetests -sv
+    displayName: Test py2bit

azure-pipelines.yml

@@ -278,6 +278,7 @@ uint8_t getByteMaskFromOffset(int offset) {
 void *twobitBasesWorker(TwoBit *tb, uint32_t tid, uint32_t start, uint32_t end, int fraction) {
     void *out;
     uint32_t tmp[4] = {0, 0, 0, 0}, len = end - start + (start % 4), i = 0, j = 0;
+    uint32_t seqLen = end - start;
     uint32_t blockStart, blockEnd, maskIdx = (uint32_t) -1, maskStart, maskEnd, foo;
     uint8_t *bytes = NULL, mask = 0, offset;
 
@@ -375,10 +376,10 @@ void *twobitBasesWorker(TwoBit *tb, uint32_t tid, uint32_t start, uint32_t end,
     //out is in TCAG order, since that's how 2bit is stored.
     //However, for whatever reason I went with ACTG in the first release...
     if(fraction) {
-        ((double*) out)[0] = ((double) tmp[2])/((double) len);
-        ((double*) out)[1] = ((double) tmp[1])/((double) len);
-        ((double*) out)[2] = ((double) tmp[0])/((double) len);
-        ((double*) out)[3] = ((double) tmp[3])/((double) len);
+        ((double*) out)[0] = ((double) tmp[2])/((double) seqLen);
+        ((double*) out)[1] = ((double) tmp[1])/((double) seqLen);
+        ((double*) out)[2] = ((double) tmp[0])/((double) seqLen);
+        ((double*) out)[3] = ((double) tmp[3])/((double) seqLen);
     } else {
         ((uint32_t*) out)[0] = tmp[2];
         ((uint32_t*) out)[1] = tmp[1];