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

spaces!!!!!!!!! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@814 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
andrewk 2009-05-26 19:40:25 +00:00
parent c2df35b7fe
commit 149cc9989b
1 changed files with 11 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java
View File

@ -51,7 +51,6 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
String dinuc_root = "dinuc"; String dinuc_root = "dinuc";
ArrayList<PrintStream> dinuc_outs = new ArrayList<PrintStream>(); ArrayList<PrintStream> dinuc_outs = new ArrayList<PrintStream>();
PrintStream covars_out = new PrintStream("covars.out");
PrintStream ByQualFile; // = new PrintStream("quality_empirical_vs_observed.csv"); PrintStream ByQualFile; // = new PrintStream("quality_empirical_vs_observed.csv");
PrintStream ByCycleFile; PrintStream ByCycleFile;
PrintStream ByDinucFile; PrintStream ByDinucFile;
@ -155,11 +154,17 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
} }
public void onTraversalDone(Integer result) { public void onTraversalDone(Integer result) {
PrintStream covars_out;
try {
covars_out = new PrintStream(OUTPUT_FILEROOT+".covars.out");
if (flattenData.size() > 0) if (flattenData.size() > 0)
covars_out.println(flattenData.get(0).headerString()); covars_out.println(flattenData.get(0).headerString());
for ( RecalData datum : flattenData ) { for ( RecalData datum : flattenData ) {
covars_out.println(datum); covars_out.println(datum);
} }
} catch (FileNotFoundException e) {
System.err.println("FileNotFoundException: " + e.getMessage());
}
qualityEmpiricalObserved(); qualityEmpiricalObserved();
qualityDiffVsCycle(); qualityDiffVsCycle();