diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java index 76b590dc1..481928169 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java @@ -51,6 +51,11 @@ import java.util.regex.Pattern; public class GenomeLocParser { private static Logger logger = Logger.getLogger(GenomeLocParser.class); + private static final Pattern regex1 = Pattern.compile("([\\w&&[^:]]+)$"); // matches case 1 + private static final Pattern regex2 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)$"); // matches case 2 + private static final Pattern regex3 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)-([\\d,]+)$"); // matches case 3 + private static final Pattern regex4 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)\\+"); // matches case 4 + // -------------------------------------------------------------------------------------------------------------- // @@ -138,10 +143,6 @@ public class GenomeLocParser { // 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000' //System.out.printf("Parsing location '%s'%n", str); - final Pattern regex1 = Pattern.compile("([\\w&&[^:]]+)$"); // matches case 1 - final Pattern regex2 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)$"); // matches case 2 - final Pattern regex3 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)-([\\d,]+)$"); // matches case 3 - final Pattern regex4 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)\\+"); // matches case 4 String contig = null; long start = 1;