zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

BugFix: byte overflow in SyntheticRead compressed base counts 

* fixed and added unit test
This commit is contained in:
Mauricio Carneiro 2011-11-21 14:50:51 -05:00
parent 44554b2bfd
commit 5ad3dfcd62
2 changed files with 6 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
public/java/src/org/broadinstitute/sting/utils/MathUtils.java
View File

@ -188,6 +188,10 @@ public class MathUtils {
return ! Double.isInfinite(val) && ! Double.isNaN(val); return ! Double.isInfinite(val) && ! Double.isNaN(val);
} }
public static double bound(double value, double minBoundary, double maxBoundary) {
return Math.max(Math.min(value, maxBoundary), minBoundary);
}
public static boolean isBounded(double val, double lower, double upper) { public static boolean isBounded(double val, double lower, double upper) {
return val >= lower && val <= upper; return val >= lower && val <= upper;
} }

4
public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java
View File

@ -16,8 +16,8 @@ public class ReadUtilsUnitTest extends BaseTest {
GATKSAMRecord read, reducedRead; GATKSAMRecord read, reducedRead;
final static String BASES = "ACTG"; final static String BASES = "ACTG";
final static String QUALS = "!+5?"; final static String QUALS = "!+5?";
final private static byte[] REDUCED_READ_COUNTS = new byte[]{10, 20, 30, 40}; final private static byte[] REDUCED_READ_COUNTS = new byte[]{10, 20, 30, 40, 1};
final private static byte[] REDUCED_READ_COUNTS_TAG = new byte[]{10, 10, 20, 30}; // just the offsets final private static byte[] REDUCED_READ_COUNTS_TAG = new byte[]{10, 10, 20, 30, -9}; // just the offsets
@BeforeTest @BeforeTest
public void init() { public void init() {