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More capabilities for the pileup 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@621 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-05-07 18:03:13 +00:00
parent 89a26a7078
commit 5a4bb76cc3
1 changed files with 23 additions and 0 deletions
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23
java/src/org/broadinstitute/sting/utils/BasicPileup.java
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@ -21,6 +21,14 @@ abstract public class BasicPileup implements Pileup {
return String.format("%s: %s %s %s", getLocation(), getRef(), getBases(), getQuals());
}
public static List<Integer> constantOffset( List<SAMRecord> reads, int i ) {
List<Integer> l = new ArrayList<Integer>(reads.size());
for ( SAMRecord read : reads ) {
l.add(i);
}
return l;
}
public static String basePileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {
StringBuilder bases = new StringBuilder();
for ( byte base : basePileup(reads, offsets)) {
@ -253,4 +261,19 @@ abstract public class BasicPileup implements Pileup {
return null;
}
public static byte consensusBase(String bases) {
String canon = bases.toUpperCase();
int ACount = Utils.countOccurances('A', bases);
int CCount = Utils.countOccurances('C', bases);
int TCount = Utils.countOccurances('T', bases);
int GCount = Utils.countOccurances('G', bases);
int m = Math.max(ACount, Math.max(CCount, Math.max(TCount, GCount)));
if ( ACount == m ) return 'A';
if ( CCount == m ) return 'C';
if ( TCount == m ) return 'T';
if ( GCount == m ) return 'G';
return 0;
}
}