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and don't allocate new 200M string every time please, just pass byte array! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@417 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-04-14 21:55:33 +00:00
parent 9d56355abe
commit baae98c6d5
1 changed files with 7 additions and 3 deletions
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10
java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java
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@ -25,10 +25,14 @@ public class AlignmentUtils {
* @return * @return
*/ */
public static int numMismatches(SAMRecord r, ReferenceSequence ref) { public static int numMismatches(SAMRecord r, ReferenceSequence ref) {
return numMismatches(r, new String(ref.getBases())); return numMismatches(r, ref.getBases());
} }
public static int numMismatches(SAMRecord r, String ref) { public static int numMismatches(SAMRecord r, String ref ) {
return numMismatches(r,ref.getBytes());
}
public static int numMismatches(SAMRecord r, byte[] ref) {
if ( r.getReadUnmappedFlag() ) return 1000000; if ( r.getReadUnmappedFlag() ) return 1000000;
int i_ref = r.getAlignmentStart()-1; // position on the ref int i_ref = r.getAlignmentStart()-1; // position on the ref
int i_read = 0; // position on the read int i_read = 0; // position on the read
@ -41,7 +45,7 @@ public class AlignmentUtils {
for ( int l = 0 ; l < ce.getLength() ; l++, i_ref++, i_read++ ) { for ( int l = 0 ; l < ce.getLength() ; l++, i_ref++, i_read++ ) {
if ( Character.toUpperCase(r.getReadString().charAt(i_read) ) == 'N' ) continue; // do not count N's ? if ( Character.toUpperCase(r.getReadString().charAt(i_read) ) == 'N' ) continue; // do not count N's ?
if ( Character.toUpperCase(r.getReadString().charAt(i_read) ) != if ( Character.toUpperCase(r.getReadString().charAt(i_read) ) !=
Character.toUpperCase(ref.charAt(i_ref)) ) mm_count++; Character.toUpperCase((char)ref[i_ref]) ) mm_count++;
} }
break; break;
case I: i_read += ce.getLength(); break; case I: i_read += ce.getLength(); break;