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Fix for added EOF in csv file 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3781 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-07-13 16:09:48 +00:00
parent 9a05e8143d
commit 3db7fbb5e9
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
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@ -77,6 +77,7 @@ class AnalyzeCovariatesCLP extends CommandLineProgram {
private final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
private final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
private final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
protected static final String EOF_MARKER = "EOF";
protected int execute() {
@ -122,7 +123,7 @@ class AnalyzeCovariatesCLP extends CommandLineProgram {
try {
for ( String line : new XReadLines(new File( RECAL_FILE )) ) {
lineNumber++;
if( COMMENT_PATTERN.matcher(line).matches() || OLD_RECALIBRATOR_HEADER.matcher(line).matches()) {
if( COMMENT_PATTERN.matcher(line).matches() || OLD_RECALIBRATOR_HEADER.matcher(line).matches() || line.equals(EOF_MARKER) ) {
; // Skip over the comment lines, (which start with '#')
}
else if( COVARIATE_PATTERN.matcher(line).matches() ) { // The line string is either specifying a covariate or is giving csv data