zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Added mappingQualPileup function for use in the verbose mode of Pileup 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@391 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-14 00:51:26 +00:00
parent bc43c0eefc
commit bb666ce392
1 changed files with 10 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
java/src/org/broadinstitute/sting/utils/Utils.java
View File

@ -148,6 +148,16 @@ public class Utils {
return quals;
}
public static ArrayList<Byte> mappingQualPileup( List<SAMRecord> reads) {
ArrayList<Byte> quals = new ArrayList(reads.size());
for ( int i = 0; i < reads.size(); i++ ) {
SAMRecord read = reads.get(i);
byte qual = (byte)read.getMappingQuality();
quals.add(qual);
}
return quals;
}
public static String qualPileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {
StringBuilder quals = new StringBuilder();
for ( int qual : qualPileup(reads, offsets)) {