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Fixed an egregious error in simpleReverseComplement wherein the RC'd string would be composed entirely of the last base. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@804 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-05-22 19:32:20 +00:00
parent 2a5be1debe
commit 454a6d1df7
1 changed files with 6 additions and 14 deletions
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20
java/src/org/broadinstitute/sting/utils/BaseUtils.java
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@ -129,10 +129,10 @@ public class BaseUtils {
} }
/** /**
* Return the complement of a base. * Return the complement of a base, or the specified base if it can't be complemented (i.e. an ambiguous base).
* *
* @param base the base [AaCcGgTt] * @param base the base [AaCcGgTt]
* @return the complementary base * @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 byte simpleComplement(char base) {
switch (base) { switch (base) {
@ -144,7 +144,7 @@ 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 '.'; default: return (byte) base;
} }
} }
@ -158,7 +158,7 @@ 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]); rcbases[i] = simpleComplement((char) bases[bases.length - 1 - i]);
} }
return rcbases; return rcbases;
@ -171,20 +171,12 @@ public class BaseUtils {
* @return the reverse complement of the String * @return the reverse complement of the String
*/ */
static public String simpleReverseComplement(String bases) { static public String simpleReverseComplement(String bases) {
char[] rcbases = new char[bases.length()]; return new String(simpleReverseComplement(bases.getBytes()));
for (int i = 0; i < bases.length(); i++) {
char base = bases.charAt(bases.length() - 1);
char rcbase = (base == 'N' || base == '.') ? base : (char) simpleComplement(base);
rcbases[i] = rcbase;
}
return new String(rcbases);
} }
/** /**
* Reverse a byte array of bases * Reverse a byte array of bases
*
* @param bases the byte array of bases * @param bases the byte array of bases
* @return the reverse of the base byte array * @return the reverse of the base byte array
*/ */