/** * Constructor used when writing an index * construct one instance for each index generated */ BAMIndexMetaData() { noCoordinateRecords = 0; newReference(); }
/** * Constructor used when writing an index * construct one instance for each index generated */ BAMIndexMetaData() { noCoordinateRecords = 0; newReference(); }
/** * Constructor used when writing an index * construct one instance for each index generated */ BAMIndexMetaData() { noCoordinateRecords = 0; newReference(); }
/** * reinitialize all data structures when the reference changes */ void startNewReference() { bins = null; if (binsSeen > 0) { Arrays.fill(index, 0); } binsSeen = 0; largestIndexSeen = -1; indexStats.newReference(); } }
/** * reinitialize all data structures when the reference changes */ void startNewReference() { bins = null; if (binsSeen > 0) { Arrays.fill(index, 0); } binsSeen = 0; largestIndexSeen = -1; indexStats.newReference(); } }
/** * reinitialize all data structures when the reference changes */ void startNewReference() { ++currentReference; // I'm not crazy about recycling this object, but that is the way it was originally written and // it helps keep track of no-coordinate read count (which shouldn't be stored in this class anyway). indexStats.newReference(); binningIndexBuilder = new BinningIndexBuilder(currentReference, sequenceDictionary.getSequence(currentReference).getSequenceLength()); } }
/** * reinitialize all data structures when the reference changes */ void startNewReference() { ++currentReference; // I'm not crazy about recycling this object, but that is the way it was originally written and // it helps keep track of no-coordinate read count (which shouldn't be stored in this class anyway). indexStats.newReference(); binningIndexBuilder = new BinningIndexBuilder(currentReference, sequenceDictionary.getSequence(currentReference).getSequenceLength()); } }
/** * reinitialize all data structures when the reference changes */ void startNewReference() { ++currentReference; // I'm not crazy about recycling this object, but that is the way it was originally written and // it helps keep track of no-coordinate read count (which shouldn't be stored in this class anyway). indexStats.newReference(); binningIndexBuilder = new BinningIndexBuilder(currentReference, sequenceDictionary.getSequence(currentReference).getSequenceLength()); } }
/** * reinitialize all data structures when the reference changes */ void startNewReference(int reference) { currentReference = reference; // I'm not crazy about recycling this object, but that is the way it was originally written and // it helps keep track of no-coordinate read count (which shouldn't be stored in this class anyway). indexStats.newReference(); binningIndexBuilder = new BinningIndexBuilder(currentReference, sequenceDictionary.getSequence(currentReference).getSequenceLength()); } }
/** * reinitialize all data structures when the reference changes */ void startNewReference(int reference) { currentReference = reference; // I'm not crazy about recycling this object, but that is the way it was originally written and // it helps keep track of no-coordinate read count (which shouldn't be stored in this class anyway). indexStats.newReference(); binningIndexBuilder = new BinningIndexBuilder(currentReference, sequenceDictionary.getSequence(currentReference).getSequenceLength()); } }