From 3db7fbb5e9aa43f4f7275f416587678144d0cb48 Mon Sep 17 00:00:00 2001 From: rpoplin Date: Tue, 13 Jul 2010 16:09:48 +0000 Subject: [PATCH] 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 --- .../sting/analyzecovariates/AnalyzeCovariates.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java b/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java index 2c6371d30..143c3e6d3 100755 --- a/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java +++ b/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java @@ -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