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Misc. additions to correct utilities 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3329 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-05-07 21:34:18 +00:00
parent 64ccaa4c6a
commit 504103bd15
2 changed files with 17 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/utils/BaseUtils.java
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@ -192,6 +192,10 @@ public class BaseUtils {
return isRegularBase((char)base); return isRegularBase((char)base);
} }
static public boolean isNBase(char base) {
return isNBase((byte)base);
}
static public boolean isNBase(byte base) { static public boolean isNBase(byte base) {
return base == 'N'; return base == 'N';
} }

13
java/src/org/broadinstitute/sting/utils/MathUtils.java
View File

@ -710,9 +710,20 @@ public class MathUtils {
} }
public static byte getQScoreMedian(List<SAMRecord> reads, List<Integer> offsets) { public static byte getQScoreMedian(List<SAMRecord> reads, List<Integer> offsets) {
return getQScoreOrderStatistic(reads, offsets, (int)Math.floor(reads.size()/2.)); return getQScoreOrderStatistic(reads, offsets, (int)Math.floor(reads.size()/2.));
} }
//
// useful common utility routines
//
public static double rate(long n, long d) { return n / (1.0 * Math.max(d, 1)); }
public static double rate(int n, int d) { return n / (1.0 * Math.max(d, 1)); }
public static long inverseRate(long n, long d) { return n == 0 ? 0 : d / Math.max(n, 1); }
public static long inverseRate(int n, int d) { return n == 0 ? 0 : d / Math.max(n, 1); }
public static double ratio(int num, int denom) { return ((double)num) / (Math.max(denom, 1)); }
public static double ratio(long num, long denom) { return ((double)num) / (Math.max(denom, 1)); }
} }