132 lines
4.2 KiB
Java
132 lines
4.2 KiB
Java
/*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2008 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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package edu.mit.broad.sam.apps;
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import edu.mit.broad.sam.SAMFileReader;
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import edu.mit.broad.sam.SAMLocusIterator;
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import edu.mit.broad.sam.SAMFileHeader;
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import java.io.File;
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import java.io.IOException;
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import java.io.Writer;
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import java.io.FileWriter;
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import java.util.List;
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public class AccumulateCoverage {
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public static void main(final String[] argv) throws Exception {
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if (argv.length != 1) {
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System.err.println("ERROR: Incorrect number of arguments");
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usage();
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System.exit(1);
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}
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final AccumulateCoverage ac = new AccumulateCoverage(argv[0]);
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}
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private static void usage() {
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System.err.println("USAGE: AccumulateCoverage <SAMFile>");
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}
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public AccumulateCoverage(final String samFile) throws IOException {
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final long startTime = System.currentTimeMillis();
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final Writer writer = new FileWriter("/Users/kcibul/projects/sam/acccov.out");
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final SAMFileReader samReader = new SAMFileReader(new File(samFile));
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// ensure the file is sorted
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//TODO: is the SAM reader implementation broken?
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if (samReader.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
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System.out.println("SAM Files must be coordinate-sorted, this is " + samReader.getFileHeader().getSortOrder());
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System.exit(1);
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}
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final SAMLocusIterator sli = new SAMLocusIterator(samReader.iterator());
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for (final SAMLocusIterator.LocusInfo li : sli) {
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String chrom = li.getChrom().substring(3);
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if (chrom.equals("M")) { chrom = "0"; }
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if (chrom.equals("X")) { chrom = "23"; }
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if (chrom.equals("Y")) { chrom = "24"; }
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final StringBuilder sb = new StringBuilder();
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sb.append(chrom)
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.append(":")
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.append(li.getPosition()-1)
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.append(" ")
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.append(li.getBases().size())
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.append("\n");
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writer.write(sb.toString());
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//System.out.print(sb);
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// // TODO: zero based or 1 based?
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// System.out.print(li.chrom + "\t" + (li.position-1) + "\t" + li.bases.size() + "\t");
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//
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// // TODO: print and capitalize by strand (like pileup)
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// System.out.print(bytesToString(li.bases));
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// System.out.print("\t");
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// System.out.print(phredToFastq(li.qualities));
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// System.out.print("\n");
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}
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writer.flush();
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writer.close();
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final long elapsed = System.currentTimeMillis() - startTime;
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System.out.println("Completed in " + elapsed + "ms");
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}
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static String bytesToString(final List<Byte> data) {
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if (data == null || data.size() == 0) {
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return null;
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}
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final char[] chars = new char[data.size()];
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for (int i = 0; i < data.size(); i++) {
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chars[i] = (char) (data.get(i) & 0xFF);
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}
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return new String(chars);
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}
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static String phredToFastq(final List<Byte> data) {
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final byte[] arrData = new byte[data.size()];
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for(int i=0; i< data.size(); i++) { arrData[i] = data.get(i); }
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return phredToFastq(arrData);
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}
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static String phredToFastq(final byte[] data) {
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if (data == null) {
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return null;
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}
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return phredToFastq(data, 0, data.length);
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}
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static String phredToFastq(final byte[] buffer, final int offset, final int length) {
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final char[] chars = new char[length];
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for (int i = 0; i < length; i++) {
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chars[i] = phredToFastq(buffer[offset+i] & 0xFF);
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}
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return new String(chars);
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}
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static char phredToFastq(final int phredScore) {
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if (phredScore < 0 || phredScore > 63) {
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throw new IllegalArgumentException("Cannot encode phred score: " + phredScore);
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}
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return (char) (33 + phredScore);
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}
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} |