BAMIndexBuilder(final SAMSequenceDictionary sequenceDictionary) { this.sequenceDictionary = sequenceDictionary; if (!sequenceDictionary.isEmpty()) startNewReference(); }
/** write out any references between the currentReference and the nextReference */ private void advanceToReference(final int nextReference) { while (currentReference < nextReference) { final BAMIndexContent content = indexBuilder.processReference(currentReference); outputWriter.writeReference(content); currentReference++; if (currentReference < numReferences) { indexBuilder.startNewReference(); } } }
/** write out any references between the currentReference and the nextReference */ private void advanceToReference(final int nextReference) { while (currentReference < nextReference) { final BAMIndexContent content = indexBuilder.processReference(currentReference); outputWriter.writeReference(content); currentReference++; if (currentReference < numReferences) { indexBuilder.startNewReference(); } } }
/** write out any references between the currentReference and the nextReference */ private void advanceToReference(final int nextReference) { while (currentReference < nextReference) { final BAMIndexContent content = indexBuilder.processReference(currentReference); outputWriter.writeReference(content); currentReference++; if (currentReference < numReferences) { indexBuilder.startNewReference(); } } }
BAMIndexBuilder(final SAMSequenceDictionary sequenceDictionary) { this.sequenceDictionary = sequenceDictionary; if (!sequenceDictionary.isEmpty()) startNewReference(); }
BAMIndexBuilder(final SAMSequenceDictionary sequenceDictionary) { this.sequenceDictionary = sequenceDictionary; if (!sequenceDictionary.isEmpty()) startNewReference(); }