returning read instead of GATKSAMRecord
Do not create new GATKSAMRecord when read has been fully clipped, because it is essentially the same as returning the currently fully clipped read.
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@ -121,7 +121,7 @@ public class ReadClipper {
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public GATKSAMRecord hardClipSoftClippedBases () {
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if (read.isEmpty())
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return new GATKSAMRecord(read.getHeader());
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return read;
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int readIndex = 0;
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int cutLeft = -1; // first position to hard clip (inclusive)
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