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Experimental refactoring. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@675 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-05-12 19:46:50 +00:00
parent 758f8aa89b
commit 095dacd154
1 changed files with 96 additions and 0 deletions
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96
java/src/org/broadinstitute/sting/playground/fourbasecaller/AddFourProbsToSAM.java 100755
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package org.broadinstitute.sting.playground.fourbasecaller;
import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.QualityUtils;
import java.io.File;
import java.util.HashMap;
import net.sf.samtools.*;
public class AddFourProbsToSAM extends CommandLineProgram {
public static AddFourProbsToSAM Instance = null;
public File UNALIGNED_SAM;
public File ALIGNED_SAM;
public File FINAL_SAM;
public int END;
public Boolean DEBUG = false;
public static void main(String[] argv) {
Instance = new AddFourProbsToSAM();
start(Instance, argv);
}
protected void setupArgs() {
//m_parser.addRequiredArg("unaligned_sam", "U", "Unaligned SAM file", "UNALIGNED_SAM");
//m_parser.addRequiredArg("aligned_sam", "A", "Aligned SAM file", "ALIGNED_SAM");
//m_parser.addRequiredArg("final_sam", "F", "Final SAM file", "FINAL_SAM");
//m_parser.addRequiredArg("end", "E", "Pair end (0 - all, 1 - first, 2 - second)", "END");
//m_parser.addOptionalFlag("debug", "D", "Turn on debugging output", "DEBUG");
}
protected int execute() {
int processed;
SAMFileReader alignedSf = new SAMFileReader(ALIGNED_SAM);
alignedSf.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
// First, hash the aligned records (because there are less of them than unaligned reads)
System.err.println("Hashing aligned records...");
HashMap<String, SAMRecord> records = new HashMap<String, SAMRecord>(10000000);
processed = 0;
for (SAMRecord alignedSr : alignedSf) {
if (END == 0 || (END == 1 && alignedSr.getSecondOfPairFlag() == false) || (END == 2 && alignedSr.getSecondOfPairFlag() == true)) {
if (!alignedSr.getReadUnmappedFlag()) {
records.put(alignedSr.getReadName(), alignedSr);
if (processed % 100000 == 0) { System.err.print("\tProcessed " + processed + " records.\r"); }
processed++;
}
}
}
// Now, iterate over the unaligned SAM file and stick the four-base probs in.
System.err.println("\nInterating over unaligned records...");
SAMFileReader unalignedSf = new SAMFileReader(UNALIGNED_SAM);
unalignedSf.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
SAMFileHeader swhead = alignedSf.getFileHeader();
swhead.setSortOrder(SAMFileHeader.SortOrder.unsorted);
SAMFileWriter sw = new SAMFileWriterFactory().makeSAMOrBAMWriter(swhead, true, FINAL_SAM);
processed = 0;
for (SAMRecord unalignedSr : unalignedSf) {
if (records.containsKey(unalignedSr.getReadName())) {
SAMRecord alignedSr = records.get(unalignedSr.getReadName());
byte[] sq = (byte[]) unalignedSr.getAttribute("SQ");
if (alignedSr.getReadNegativeStrandFlag()) {
sq = QualityUtils.reverseComplementCompressedQualityArray(sq);
}
alignedSr.setAttribute("SQ", sq);
alignedSr.setAttribute("KB", unalignedSr.getReadBases());
alignedSr.setAttribute("KQ", unalignedSr.getBaseQualities());
sw.addAlignment(alignedSr);
if (DEBUG) {
System.out.println(alignedSr.format());
}
if (processed % 100000 == 0) { System.err.print("\tProcessed " + processed + " records.\r"); }
processed++;
}
}
sw.close();
alignedSf.close();
unalignedSf.close();
return 0;
}
}