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Fix edge case for very small VCFs

This commit is contained in:
Christopher Hartl 2012-01-19 00:51:28 -05:00
parent 1e037a0ecf
commit 39e6df5aa9
1 changed files with 15 additions and 15 deletions
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6
public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala
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@ -26,9 +26,6 @@ class VCFExtractIntervals(inVCF: File, outList: File, useFilterSites: Boolean) e
var cur : String = null var cur : String = null
if ( elems.hasNext ) { if ( elems.hasNext ) {
cur = elems.next cur = elems.next
} else {
out.printf("%s%n",prev)
}
while ( elems.hasNext ) { while ( elems.hasNext ) {
out.printf("%s%n",prev) out.printf("%s%n",prev)
while ( cur.equals(prev) && elems.hasNext && !cur.equals("") ) { while ( cur.equals(prev) && elems.hasNext && !cur.equals("") ) {
@ -44,6 +41,9 @@ class VCFExtractIntervals(inVCF: File, outList: File, useFilterSites: Boolean) e
} }
out.printf("%s%n",prev) out.printf("%s%n",prev)
out.printf("%s%n",cur) out.printf("%s%n",cur)
} else {
out.printf("%s%n",prev)
}
out.close out.close
} }