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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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30
public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala
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@ -26,24 +26,24 @@ class VCFExtractIntervals(inVCF: File, outList: File, useFilterSites: Boolean) e
var cur : String = null
if ( elems.hasNext ) {
cur = elems.next
while ( elems.hasNext ) {
out.printf("%s%n",prev)
while ( cur.equals(prev) && elems.hasNext && !cur.equals("") ) {
cur = elems.next
}
if ( ! cur.equals(prev) ) {
if ( elems.hasNext ) {
prev = cur
cur = elems.next
}
}
}
out.printf("%s%n",prev)
out.printf("%s%n",cur)
} else {
out.printf("%s%n",prev)
}
while ( elems.hasNext ) {
out.printf("%s%n",prev)
while ( cur.equals(prev) && elems.hasNext && !cur.equals("") ) {
cur = elems.next
}
if ( ! cur.equals(prev) ) {
if ( elems.hasNext ) {
prev = cur
cur = elems.next
}
}
}
out.printf("%s%n",prev)
out.printf("%s%n",cur)
out.close
}