/** * Alternative to other one with similar name * * @param directory directory containing SDF * @param indexFile index file * @param loadNames should we load names * @param loadFullNames should we load full names * @param region region to restrict to * @throws IOException IO exception occurs */ CompressedMemorySequencesReader2( File directory, IndexFile indexFile, boolean loadNames, boolean loadFullNames, LongRange region) throws IOException { mIndexFile = indexFile; mRegion = SequencesReaderFactory.resolveRange(indexFile, region); mStart = mRegion.getStart(); mEnd = mRegion.getEnd(); mNumberSequences = mEnd - mStart; mData = DataInMemory.loadDelayQuality( directory, indexFile, DataFileIndex.loadSequenceDataFileIndex(indexFile.dataIndexVersion(), directory), mStart, mEnd); if (mNumberSequences > Integer.MAX_VALUE) { throw new IllegalArgumentException( "Too many sequences in region: " + region + ", maximum is: " + Integer.MAX_VALUE); } mDirectory = directory; if (loadNames && mIndexFile.hasNames()) { loadNames(); loadNameSuffixes(loadFullNames, mIndexFile.hasSequenceNameSuffixes()); } final StringBuilder sb = new StringBuilder("CMSR2 statistics"); sb.append(LS); this.infoString(sb); Diagnostic.userLog(sb.toString()); }