From d3165a7c21ce65459ecbf87c1cbd81713a77fc5a Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 29 Mar 2012 16:18:12 +0100
Subject: [PATCH] use hashmap and fix read count
---
uk/ac/sanger/artemis/components/alignment/BamUtils.java | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamUtils.java b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
index ee271b58f..6ae9a7916 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamUtils.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
@@ -23,6 +23,7 @@
*/
package uk.ac.sanger.artemis.components.alignment;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.Vector;
@@ -71,9 +72,9 @@ class BamUtils
final String refName,
final Hashtable<String, SAMFileReader> samFileReaderHash,
final Vector<String> seqNames,
- final Hashtable<String, Integer> offsetLengths,
+ final HashMap<String, Integer> offsetLengths,
final boolean concatSequences,
- final Hashtable<String, Integer> seqLengths,
+ final HashMap<String, Integer> seqLengths,
final SAMRecordPredicate samRecordFlagPredicate,
final SAMRecordMapQPredicate samRecordMapQPredicate,
final boolean contained)
@@ -91,7 +92,7 @@ class BamUtils
if( (lastLen >= start && lastLen < end) ||
(len >= start && len < end) ||
(start >= lastLen && start < len) ||
- (end >= lastLen && end < len) )
+ (end > lastLen && end < len) )
{
int offset = offsetLengths.get(name);
int thisStart = start - offset;
--
GitLab