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

Further protection vs null pointers in PrintReadsWalker

This commit is contained in:
Guillermo del Angel 2011-07-19 21:59:24 -04:00
parent fb2d475c22
commit e8409c80fa
1 changed files with 2 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
View File

@ -59,9 +59,9 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
@Argument(fullName = "number", shortName = "n", doc="Print the first n reads from the file, discarding the rest", required = false) @Argument(fullName = "number", shortName = "n", doc="Print the first n reads from the file, discarding the rest", required = false)
int nReadsToPrint = -1; int nReadsToPrint = -1;
@Argument(fullName="sample_file", shortName="sf", doc="File containing a list of samples (one per line). Can be specified multiple times", required=false) @Argument(fullName="sample_file", shortName="sf", doc="File containing a list of samples (one per line). Can be specified multiple times", required=false)
public Set<File> sampleFile; public Set<File> sampleFile = new TreeSet<File>();
@Argument(fullName="sample_name", shortName="sn", doc="Sample name to be included in the analysis. Can be specified multiple times.", required=false) @Argument(fullName="sample_name", shortName="sn", doc="Sample name to be included in the analysis. Can be specified multiple times.", required=false)
public Set<String> sampleNames; public Set<String> sampleNames = new TreeSet<String>();
private TreeSet<String> samplesToChoose = new TreeSet<String>(); private TreeSet<String> samplesToChoose = new TreeSet<String>();
private boolean NO_SAMPLES_SPECIFIED = false; private boolean NO_SAMPLES_SPECIFIED = false;