Package net.sf.picard.reference

Examples of net.sf.picard.reference.ReferenceSequenceFile.nextSequence()

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    final Map<SNPCallPair, TreeMap<Integer, Long>> calltable_validation = new HashMap<SNPCallPair, TreeMap<Integer, Long>>();

    ReferenceSequence reference = null;

    while ((reference = reference_file.nextSequence()) != null) {
      for (SamPositionIterator position_iterator : positionIterators) {
        position_iterator.nextSequence();
        String ref_name = reference.getName();

        if (!position_iterator.getCurrentSequence().equals(ref_name))
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