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Added a method to reverse-complement a String object, preserving 'N' and '.' bases. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@776 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-05-21 19:39:39 +00:00
parent 1a3ca97d29
commit 1a9d5cea29
1 changed files with 21 additions and 1 deletions
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22
java/src/org/broadinstitute/sting/utils/BaseUtils.java
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@ -112,7 +112,8 @@ public class BaseUtils {
} }
/** /**
* Reverse complement a byte array of bases * Reverse complement a byte array of bases (that is, chars casted to bytes, *not* base indices in byte form)
*
* @param bases the byte array of bases * @param bases the byte array of bases
* @return the reverse complement of the base byte array * @return the reverse complement of the base byte array
*/ */
@ -126,6 +127,25 @@ public class BaseUtils {
return rcbases; return rcbases;
} }
/**
* Reverse complement a String of bases. Preserves ambiguous bases.
*
* @param bases the String of bases
* @return the reverse complement of the String
*/
static public String simpleReverseComplement(String bases) {
char[] rcbases = new char[bases.length()];
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