Commit 2643aa2b authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Fix insertsize report (missing sentence)

parent f6796a24
......@@ -89,10 +89,10 @@ object SeqStat extends ToolCommand {
(qual_low_boundery < 59, qual_high_boundery > 74) match {
case (false, true) => phredEncoding = Solexa
// TODO: check this later on
// complex case, we cannot tell wheter this is a sanger or solexa
// but since the qual_high_boundery exceeds any Sanger/Illumina1.8 quals, we can `assume` this is solexa
// New @ 2016/01/26: Illumina X ten samples can contain Phred=Q42 (qual_high_boundery==75/K)
// TODO: check this later on
// complex case, we cannot tell wheter this is a sanger or solexa
// but since the qual_high_boundery exceeds any Sanger/Illumina1.8 quals, we can `assume` this is solexa
// New @ 2016/01/26: Illumina X ten samples can contain Phred=Q42 (qual_high_boundery==75/K)
case (true, true) => phredEncoding = Solexa
// this is definite a sanger sequence, the lower end is sanger only
case (true, false) => phredEncoding = Sanger
......@@ -130,8 +130,8 @@ object SeqStat extends ToolCommand {
baseStats ++= mutable.ArrayBuffer.fill(record.length - baseStats.length)(BaseStat())
}
if (readStats.lengths.length < record.length) {
readStats.lengths ++= mutable.ArrayBuffer.fill(record.length - readStats.lengths.length + 1)(0)
if (readStats.lengths.length < record.length + 1) {
readStats.lengths ++= mutable.ArrayBuffer.fill((record.length + 1) - readStats.lengths.length)(0)
}
val readQuality = record.getBaseQualityString
......@@ -181,7 +181,7 @@ object SeqStat extends ToolCommand {
quals ++= mutable.ArrayBuffer.fill(baseStats(pos).qual.length - quals.length)(0)
}
if (nucs.length <= baseStats(pos).nucs.length) {
nucs ++= mutable.ArrayBuffer.fill( baseStats(pos).nucs.length - nucs.length )(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 }
......
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