From e8186cf3a7b784dbe416492e41c409f9afd8699f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 9 Mar 2015 10:38:16 +0100
Subject: [PATCH] Fix array out of bound error
---
.../src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala | 3 +++
1 file changed, 3 insertions(+)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
index 353cbaab7..822487bf9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
@@ -194,6 +194,9 @@ object Seqstat extends ToolCommand {
val readQual = record.getBaseQualityString
val readNucleotides = record.getReadString
+ if (record.length >= readStats.lengths.size) // Extends array when length not yet possible
+ (0 to (record.length - readStats.lengths.size)).foreach(_ => readStats.lengths.append(0))
+
readStats.lengths(record.length) += 1
for (t <- 0 until record.length()) {
--
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