/** * initialize the iterator to an unmapped read position */ public void initializeUnmapped() { // throw away data from the previous invocation, if one exists. ensureUntouched(); reset(); while (super.hasNext() && this.peek().getReferenceIndex() >= 0) { super.next(); } // sanity check that we have an actual matching read next SAMRecord rec = this.peek(); if (rec == null) { throw new ReviewedGATKException("The next read doesn't match"); } // set the seeked variable to true seeked = true; }
ensureUntouched(); reset();