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

Added ION Torrent support to CountCovariates.

This commit is contained in:
Mauricio Carneiro 2011-10-12 01:57:02 -04:00
parent a2733a451f
commit e53a952aeb
1 changed files with 3 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
View File

@ -164,6 +164,7 @@ public class CycleCovariate implements StandardCovariate {
private static List<String> LS454_NAMES = Arrays.asList("454");
private static List<String> COMPLETE_GENOMICS_NAMES = Arrays.asList("COMPLETE");
private static List<String> PACBIO_NAMES = Arrays.asList("PACBIO");
private static List<String> ION_TORRENT_NAMES = Arrays.asList("IONTORRENT");
private static boolean isPlatform(SAMRecord read, List<String> names) {
String pl = read.getReadGroup().getPlatform().toUpperCase();
@ -224,10 +225,10 @@ public class CycleCovariate implements StandardCovariate {
}
//-----------------------------
// 454
// 454 and Ion Torrent
//-----------------------------
else if ( isPlatform(read, LS454_NAMES) ) { // Some bams have "LS454" and others have just "454"
else if ( isPlatform(read, LS454_NAMES) || isPlatform(read, ION_TORRENT_NAMES)) { // Some bams have "LS454" and others have just "454"
final int readLength = read.getReadLength();
final byte[] bases = read.getReadBases();