From 0886c76f3c8a5177fcee354133226f20b8f3fc68 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 11 Nov 2014 15:00:59 +0100
Subject: [PATCH] Added general vcf utils
---
.../nl/lumc/sasc/biopet/util/VcfUtils.scala | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
create mode 100644 biopet-framework/src/main/scala/nl/lumc/sasc/biopet/util/VcfUtils.scala
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/util/VcfUtils.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/util/VcfUtils.scala
new file mode 100644
index 000000000..c91f5b2a0
--- /dev/null
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/util/VcfUtils.scala
@@ -0,0 +1,19 @@
+package nl.lumc.sasc.biopet.util
+
+import htsjdk.variant.variantcontext.VariantContext
+import scala.collection.JavaConversions._
+
+/** Utility object for general vcf file/records functions. */
+object VcfUtils {
+ /**
+ * Return longest allele of VariantContext.
+ *
+ * @param vcfRecord record to check
+ * @return allele with most nucleotides
+ */
+ def getLongestAllele(vcfRecord: VariantContext) = {
+ val alleles = vcfRecord.getAlleles
+ val longestAlleleId = alleles.map(_.getBases.length).zipWithIndex.maxBy(_._1)._2
+ alleles(longestAlleleId)
+ }
+}
--
GitLab