From ef2ea799948c4ad4d6e8fc8d5b148bd4c6f561b5 Mon Sep 17 00:00:00 2001 From: depristo Date: Tue, 27 Oct 2009 21:53:40 +0000 Subject: [PATCH] code cleanup and containsStartPosition function git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1919 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/utils/GenomeLoc.java | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java index 69c11ba83..0dc66f055 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java @@ -1,10 +1,10 @@ package org.broadinstitute.sting.utils; import net.sf.samtools.SAMRecord; -import org.apache.log4j.Logger; import java.util.ArrayList; import java.util.List; +import java.io.Serializable; /** * Created by IntelliJ IDEA. @@ -16,9 +16,7 @@ import java.util.List; * * */ -public class GenomeLoc implements Comparable, Cloneable { - private static Logger logger = Logger.getLogger(GenomeLoc.class); - +public class GenomeLoc implements Comparable, Cloneable, Serializable { /** * the basic components of a genome loc, its contig index, * start and stop position, and (optionally) the contig name @@ -178,6 +176,15 @@ public class GenomeLoc implements Comparable, Cloneable { return onSameContig(that) && getStart() <= that.getStart() && getStop() >= that.getStop(); } + /** + * Returns true if this GenomeLoc contains the start position of GenomeLoc that, on the same contig + * @param start + * @return + */ + public final boolean containsStartPosition(long start) { + return getStart() <= start && start <= getStop(); + } + public final boolean onSameContig(GenomeLoc that) { return (this.contigIndex == that.contigIndex); }