diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala index 6b31714e809915120d80002591d2d9f7c1a6c9e6..e4bfab05b3f0a8014f8d8820f72d91167e45b28e 100644 --- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala +++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala @@ -136,9 +136,6 @@ object SeqStat extends ToolCommand { val readQuality = 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()) { @@ -183,7 +180,7 @@ object SeqStat extends ToolCommand { quals ++= mutable.ArrayBuffer.fill(baseStats(pos).qual.length - quals.length)(0) } if (nucs.length <= baseStats(pos).nucs.length) { - for (_ <- nucs.length until baseStats(pos).nucs.length) nucs.append(0) + nucs ++= mutable.ArrayBuffer.fill( baseStats(pos).nucs.length - nucs.length )(0) } // count into the quals baseStats(pos).qual.zipWithIndex foreach { case (value, index) => quals(index) += value }