Merge pull request #11 from dpryan79/issue10

Address #10, don't write 4 bytes if fewer were requested

Author: dpryan79

.github/workflows/test.yml

@@ -0,0 +1,19 @@
+name: Test
+on:
+  pull_request:
+
+jobs:
+  testLinux:
+    name: Test Linux
+    runs-on: "ubuntu-latest"
+    steps:
+      - uses: actions/checkout@v2
+      - run: |
+          make && make test
+  testOSX:
+    name: Test OSX
+    runs-on: "macos-latest"
+    steps:
+      - uses: actions/checkout@v2
+      - run: |
+          make && make test

.travis.yml

@@ -69,7 +69,7 @@ void bytes2bases(char *seq, uint8_t *byte, uint32_t sz, int offset) {
 
     // Deal with the first partial byte
     if(offset != 0) {
-        while(offset < 4) {
+        while(offset < 4 && pos < sz) {
            seq[pos++] = byte2base(foo, offset++);
         }
         if(pos >= sz) return;

2bit.c

@@ -0,0 +1,12 @@
+0	chr1	150 offset 0x4a
+1	chr2	100 offset 0x88
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACGTACGTACGTagctagctGATCGATCGTAGCTAGCTAGCTAGCTGATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNACGTACGTACGTagctagctGATC
+0	0.080000
+1	0.080000
+2	0.086667
+3	0.086667
+0	0.120000
+1	0.120000
+2	0.120000
+3	0.120000

test/expected

@@ -9,12 +9,9 @@
 # N.B., this MUST be run from within the source directory!
 
 # Read test
-p1 = Popen(["./test/exampleRead", "test/foo.2bit"], stdout=PIPE)
-try:
-    p2 = Popen(["md5sum"], stdin=p1.stdout, stdout=PIPE)
-except:
-    p2 = Popen(["md5"], stdin=p1.stdout, stdout=PIPE)
-md5sum = p2.communicate()[0].strip().split()[0]
-assert(md5sum == "0274c32c7f3dd75e8991f6107dca6a5f")
+o = open("test/found", "w")
+check_call(["./test/exampleRead", "test/foo.2bit"], stdout=o)
+o.close()
+check_call(["diff", "test/found", "test/expected"])
 
 print("Passed!")