/**
* 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());
}
@Override
public int read(long sequenceIndex, byte[] dataOut) throws IllegalArgumentException, IOException {
if (sequenceIndex >= mNumberSequences) {
throw new IllegalArgumentException(
"Invalid sequence index: " + sequenceIndex + ", maximum is: " + mNumberSequences);
}
return mData.readSequence((int) sequenceIndex, dataOut, 0, Integer.MAX_VALUE);
}
@Override
public int readQuality(long sequenceIndex, byte[] dest, int start, int length)
throws IllegalArgumentException, IOException {
if (sequenceIndex >= mNumberSequences) {
throw new IllegalArgumentException(
"Invalid sequence index: " + sequenceIndex + ", maximum is: " + mNumberSequences);
}
return mData.readQuality((int) sequenceIndex, dest, start, length);
}
@Override
public int[] sequenceLengths(long start, long end) {
if (start >= mNumberSequences) {
throw new IllegalArgumentException(
"Invalid sequence index: " + start + ", maximum is: " + mNumberSequences);
}
if (end > mNumberSequences) {
throw new IllegalArgumentException(
"Invalid sequence index: " + end + ", maximum is: " + mNumberSequences);
}
return mData.sequenceLengths((int) start, (int) end);
}
void infoString(final StringBuilder sb) {
sb.append("Memory Usage: ").append(mNumberSequences).append(" sequences").append(LS);
long totalBytes = mData.infoString(sb);
if (mNames != null) {
sb.append("\t\t")
.append(StringUtils.commas(mNames.bytes()))
.append("\t")
.append(StringUtils.commas(mNames.length()))
.append("\tNames")
.append(LS);
totalBytes += mNames.bytes();
}
if (mNameSuffixes != null) {
sb.append("\t\t")
.append(StringUtils.commas(mNameSuffixes.bytes()))
.append("\t")
.append(StringUtils.commas(mNameSuffixes.length()))
.append("\tSuffixes")
.append(LS);
totalBytes += mNameSuffixes.bytes();
}
sb.append("\t\t").append(StringUtils.commas(totalBytes)).append("\t\tTotal bytes").append(LS);
}
void initQuality() throws IOException {
mData.initQuality();
}
@Override
public byte sequenceDataChecksum(long sequenceIndex) throws IOException {
return mData.sequenceChecksum((int) sequenceIndex);
}
@Override
public int length(long sequenceIndex) {
return mData.length((int) sequenceIndex);
}