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Trival consistency change from char in to char out, not char in to byte out 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1466 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-08-27 23:37:37 +00:00
parent 6012f7602b
commit a639459112
2 changed files with 4 additions and 4 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
View File

@ -208,7 +208,7 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
if (base == 'T'){numTs++;} if (base == 'T'){numTs++;}
if (base == 'G'){numGs++;} if (base == 'G'){numGs++;}
//consider base in likelihood calculations if it looks good and has high mapping score //consider base in likelihood calculations if it looks good and has high mapping score
G.add(base, qual); G.add(base, qual, ! read.getReadNegativeStrandFlag());
} }
} }

6
java/src/org/broadinstitute/sting/utils/BaseUtils.java
View File

@ -197,7 +197,7 @@ public class BaseUtils {
* @param base the base [AaCcGgTt] * @param base the base [AaCcGgTt]
* @return the complementary base, or the input base if it's not one of the understood ones * @return the complementary base, or the input base if it's not one of the understood ones
*/ */
static public byte simpleComplement(char base) { static public char simpleComplement(char base) {
switch (base) { switch (base) {
case 'A': case 'A':
case 'a': return 'T'; case 'a': return 'T';
@ -207,7 +207,7 @@ public class BaseUtils {
case 'g': return 'C'; case 'g': return 'C';
case 'T': case 'T':
case 't': return 'A'; case 't': return 'A';
default: return (byte) base; default: return base;
} }
} }
@ -221,7 +221,7 @@ public class BaseUtils {
byte[] rcbases = new byte[bases.length]; byte[] rcbases = new byte[bases.length];
for (int i = 0; i < bases.length; i++) { for (int i = 0; i < bases.length; i++) {
rcbases[i] = simpleComplement((char) bases[bases.length - 1 - i]); rcbases[i] = (byte)simpleComplement((char) bases[bases.length - 1 - i]);
} }
return rcbases; return rcbases;