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Now that we always reserve space for two read ends when collecting stats stratified by libraries, we need to check that the second end was indeed present; otherwise the pointer is null and this was causing an exception 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3656 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-06-28 16:40:16 +00:00
parent 26ef1f84bf
commit cc8d8eaedb
1 changed files with 4 additions and 4 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java
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@ -98,7 +98,7 @@ public class CycleQualityWalker extends ReadWalker<Integer,Integer> {
// if end == 0 (single end lane), we allocate array of length 1, otherwise we need two
// elements in the array in order to be able to collect statistics for each end in the pair independently
if ( byLane == null ) laneMap.put(lane,byLane = new CycleStats[(end==0?1:2)]);
if ( byLib == null ) libMap.put(library, byLib =new CycleStats[(end==0?1:2)]);
if ( byLib == null ) libMap.put(library, byLib =new CycleStats[2]);
if ( end != 0 ) end--; // we will now use 'end' as index into the array of stats
@ -195,7 +195,7 @@ public class CycleQualityWalker extends ReadWalker<Integer,Integer> {
for( Map.Entry<String,CycleStats[]> e : m.entrySet() ) {
if ( e.getValue()[0].getMaxReadLength() > maxLength ) maxLength = e.getValue()[0].getMaxReadLength();
if ( e.getValue().length == 1 ) {
if ( e.getValue().length == 1 || e.getValue().length == 2 && e.getValue()[1] == null ) {
totalReads_unpaired += e.getValue()[0].getReadCount(); // single end lane
} else {
totalReads_1 += e.getValue()[0].getReadCount();
@ -233,7 +233,7 @@ public class CycleQualityWalker extends ReadWalker<Integer,Integer> {
int minL = ( end1 == null ? 0 : end1.getMinReadLength() );
int maxL = ( end1 == null ? 0 : end1.getMaxReadLength() );
if ( data.length == 2 ) {
if ( data.length == 2 && data[1] != null ) {
out.println(": paired");
if ( HTML ) out.println("<br>");
out.println(" Reads analyzed:");
@ -292,7 +292,7 @@ public class CycleQualityWalker extends ReadWalker<Integer,Integer> {
w.write(String.format("%.4f",aq));
recordProblem(aq,cycle, problems,col+".End1");
}
if ( data.length > 1 ) {
if ( data.length > 1 && data[1] != null ) {
w.write('\t');
CycleStats end2 = data[1];
if ( end2 == null || cycle >= end2.getMaxReadLength() ) w.write('.');