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/*
* The MIT License
*
* Copyright (c) 2010 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.PrintWriter;
import java.util.List;
/**
* Class for writing binary BAM index files as human-readable text.
* Used for testing only.
*/
class TextualBAMIndexWriter implements BAMIndexWriter {
protected final int nRef;
protected final File output;
private final PrintWriter pw;
private int count = 0;
/**
* constructor
*
* @param nRef Number of reference sequences
* @param output BAM Index output file
*/
public TextualBAMIndexWriter(final int nRef, final File output) {
this.output = output;
this.nRef = nRef;
try {
pw = new PrintWriter(output);
} catch (final FileNotFoundException e) {
throw new SAMException("Can't find output file " + output, e);
}
writeHeader();
}
/**
* Write header information at the beginning of the file
*/
private void writeHeader() {
pw.println("n_ref=" + nRef);
}
/**
* Write this content as human-readable text
*/
@Override
public void writeReference(final BAMIndexContent content) {
final int reference = content.getReferenceSequence();
if (content == null) {
writeNullContent(reference);
count++;
return;
}
if (reference != count){
throw new SAMException("Reference on content is " + reference + " but expecting reference " + count);
}
count++;
final BAMIndexContent.BinList bins = content.getBins();
final int size = bins == null ? 0 : content.getNumberOfNonNullBins();
if (size == 0) {
writeNullContent(reference);
return;
}
//final List chunks = content.getMetaData() == null ? null
// : content.getMetaData().getMetaDataChunks();
final BAMIndexMetaData metaData = content.getMetaData();
pw.println("Reference " + reference + " has n_bin= " + Integer.toString(size + (metaData != null? 1 : 0)));
// chunks
for (final Bin bin : bins) { // note, bins will always be sorted
if (bin.getBinNumber() == GenomicIndexUtil.MAX_BINS) break;
if (bin.getChunkList() == null) {
pw.println(" Ref " + reference + " bin " + bin.getBinNumber() + " has no binArray"); // remove?
continue;
}
final List chunkList = bin.getChunkList();
if (chunkList == null) {
pw.println(" Ref " + reference + " bin " + bin.getBinNumber() + " has no chunkList");
continue;
}
pw.print(" Ref " + reference + " bin " + bin.getBinNumber() + " has n_chunk= " + chunkList.size());
if (chunkList.isEmpty()) {
pw.println();
}
for (final Chunk c : chunkList) {
pw.println(" Chunk: " + c.toString() +
" start: " + Long.toString(c.getChunkStart(), 16) +
" end: " + Long.toString(c.getChunkEnd(), 16));
}
}
writeChunkMetaData(reference, metaData);
// linear index
final LinearIndex linearIndex = content.getLinearIndex();
if (linearIndex == null || linearIndex.getIndexEntries() == null) {
pw.println("Reference " + reference + " has n_intv= 0");
return;
}
final long[] entries = linearIndex.getIndexEntries();
final int indexStart = linearIndex.getIndexStart();
// System.out.println("index start is " + indexStart);
final int n_intv = entries.length + indexStart;
pw.println("Reference " + reference + " has n_intv= " + n_intv);
for (int k = 0; k < entries.length; k++) {
if (entries[k] != 0) {
pw.println(" Ref " + reference + " ioffset for " + (k + indexStart) + " is " + Long.toString(entries[k]));
}
}
pw.flush (); // write each reference to disk as it's being created
}
/**
* Write the meta data represented by the chunkLists associated with bin MAX_BINS 37450
*
* @param metaData information describing numAligned records, numUnAligned, etc
*/
private void writeChunkMetaData(final int reference, final BAMIndexMetaData metaData) {
final int nChunks = metaData == null ? 0 : 2;
pw.print(" Ref " + reference + " bin 37450 has n_chunk= " + nChunks);
if (nChunks == 0) {
pw.println();
} else {
pw.println(" Chunk: " + // c.toString() +
" start: " + Long.toString(metaData.getFirstOffset(), 16) +
" end: " + Long.toString(metaData.getLastOffset(), 16));
pw.println(" Chunk: " + // c.toString() +
" start: " + Long.toString(metaData.getAlignedRecordCount(), 16) +
" end: " + Long.toString(metaData.getUnalignedRecordCount(), 16));
}
}
private void writeNullContent(final int reference) {
pw.println("Reference " + reference + " has n_bin=0");
pw.println("Reference " + reference + " has n_intv=0");
}
/**
* Write count of records without coordinates
*
* @param noCoordinateCount the count of records seen with no coordinate positions in the start coordinate
*/
@Override
public void writeNoCoordinateRecordCount(final Long noCoordinateCount) {
pw.println("No Coordinate Count=" + noCoordinateCount);
}
/**
* Any necessary processing at the end of the file
*/
@Override
public void close() {
pw.close();
}
}
