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gatk-3.8
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bug fixes

This commit is contained in:
Guillermo del Angel 2011-07-04 20:45:10 -04:00
parent 7a04872a3f
commit 04df153f47
1 changed files with 6 additions and 3 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -245,11 +245,14 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
afBreakpoints = new ArrayList<Double>(); afBreakpoints = new ArrayList<Double>();
afBoosts = new ArrayList<Double>(); afBoosts = new ArrayList<Double>();
logger.info("Reading in AF boost table..."); logger.info("Reading in AF boost table...");
boolean firstLine = false;
for ( final String line : new XReadLines( AF_FILE ) ) { for ( final String line : new XReadLines( AF_FILE ) ) {
//System.out.println(line); if (!firstLine) {
final String[] vals = line.split("\t"); firstLine = true;
if (vals[0].matches("midpoints"))
continue; continue;
}
final String[] vals = line.split("\t");
double bkp = Double.valueOf(vals[0]); double bkp = Double.valueOf(vals[0]);
double afb = Double.valueOf(vals[1]); double afb = Double.valueOf(vals[1]);
afBreakpoints.add(bkp); afBreakpoints.add(bkp);