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ReduceReads ref bases are now output as '=' to save space 

Restructured the sliding window framework to manipulate a wrapped version of the SAMRecord that contains information about the reference.
This commit is contained in:
Mauricio Carneiro 2011-10-30 11:57:52 -04:00
parent dbd8c25787
commit 389380a590
1 changed files with 756 additions and 745 deletions
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23
public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
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@ -198,15 +198,13 @@ public class AlignmentUtils {
return sum;
}
/** Returns the number of mismatches in the pileup element within the given reference context.
/** Returns the mismatches in the read within the given reference context.
*
* @param read the SAMRecord
* @param ref the reference context
* @param maxMismatches the maximum number of surrounding mismatches we tolerate to consider a base good
* @param windowSize window size (on each side) to test
* @return a bitset representing which bases are good
* @return each base is represented by a bit in the BitSet. True for mismatch, false for ref
*/
public static BitSet mismatchesInRefWindow(SAMRecord read, ReferenceContext ref, int maxMismatches, int windowSize) {
public static BitSet mismatchesInRefWindow(SAMRecord read, ReferenceContext ref) {
// first determine the positions with mismatches
int readLength = read.getReadLength();
BitSet mismatches = new BitSet(readLength);
@ -214,7 +212,7 @@ public class AlignmentUtils {
// it's possible we aren't starting at the beginning of a read,
// and we don't need to look at any of the previous context outside our window
// (although we do need future context)
int readStartPos = Math.max(read.getAlignmentStart(), ref.getLocus().getStart() - windowSize);
int readStartPos = read.getAlignmentStart();
int currentReadPos = read.getAlignmentStart();
byte[] refBases = ref.getBases();
@ -265,9 +263,22 @@ public class AlignmentUtils {
break;
}
}
return mismatches;
}
/** Returns a BitSet showing what bases are good according to the criteria of maxMismatches in the window
*
* @param read the SAMRecord
* @param ref the reference context
* @param maxMismatches the maximum number of surrounding mismatches we tolerate to consider a base good
* @param windowSize window size (on each side) to test
* @return a bitset representing which bases are good
*/
public static BitSet mismatchesInRefWindow(SAMRecord read, ReferenceContext ref, int maxMismatches, int windowSize) {
int readLength = read.getReadLength();
// all bits are set to false by default
BitSet result = new BitSet(readLength);
BitSet mismatches = mismatchesInRefWindow(read, ref);
int currentPos = 0, leftPos = 0, rightPos;
int mismatchCount = 0;