Deleted the old file

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@427 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSource.java

@@ -1,127 +0,0 @@
-package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
-
-import edu.mit.broad.picard.sam.SamFileHeaderMerger;
-import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMFileReader;
-import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.iterators.MergingSamRecordIterator2;
-import org.broadinstitute.sting.utils.GenomeLoc;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * User: aaron
- * Date: Mar 26, 2009
- * Time: 2:36:16 PM
- * <p/>
- * The Broad Institute
- * SOFTWARE COPYRIGHT NOTICE AGREEMENT
- * This software and its documentation are copyright 2009 by the
- * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
- * <p/>
- * This software is supplied without any warranty or guaranteed support whatsoever. Neither
- * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
- */
-public class SAMBAMDataSource implements SimpleDataSource {
-    /** our SAM data files */
-    private final SAMFileHeader.SortOrder SORT_ORDER = SAMFileHeader.SortOrder.coordinate;
-
-    /** our log, which we want to capture anything from this class */
-    protected static Logger logger = Logger.getLogger(SAMBAMDataSource.class);
-
-    // are we set to locus mode or read mode for dividing
-    private boolean locusMode = false;
-
-    // How strict should we be with SAM/BAM parsing?
-    protected SAMFileReader.ValidationStringency strictness = SAMFileReader.ValidationStringency.STRICT;
-
-    // our list of readers
-    private final List<File> samFileList = new ArrayList<File>();
-
-    /**
-     * constructor, given a single sam file
-     *
-     * @param samFiles the list of sam files
-     */
-    public SAMBAMDataSource(List<String> samFiles) throws SimpleDataSourceLoadException {
-        for (String fileName : samFiles) {
-            File smFile = new File(fileName);
-            if (!smFile.canRead()) {
-                throw new SimpleDataSourceLoadException("SAMBAMDataSource: Unable to load file: " + fileName);
-            }
-            samFileList.add(smFile);
-
-        }
-
-        //SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(samFileList, SORT_ORDER);
-    }
-
-
-    protected SAMFileReader initializeSAMFile(final File samFile) {
-        if (samFile.toString().endsWith(".list")) {
-            return null;
-        } else {
-            SAMFileReader samReader = new SAMFileReader(samFile, true);
-            samReader.setValidationStringency(strictness);
-
-            final SAMFileHeader header = samReader.getFileHeader();
-            logger.info(String.format("Sort order is: " + header.getSortOrder()));
-
-            return samReader;
-        }
-    }
-
-
-    /**
-     * set the mode to by loci, which let's you duplicate reads, but never at a single
-     * locus, or false for read mode where no read is seen twice.
-     *
-     * @param tr true if by loci, false if by read
-     */
-    public void setToByLociMode(boolean tr) {
-        locusMode = tr;
-    }
-
-    /**
-     * <p>
-     * seek
-     * </p>
-     *
-     * @param location the genome location to extract data for
-     * @return an iterator for that region
-     */
-    public MergingSamRecordIterator2 seek(GenomeLoc location) throws SimpleDataSourceLoadException {
-
-        // right now this is pretty damn heavy, it copies the file list into a reader list every time
-        List<SAMFileReader> lst = new ArrayList<SAMFileReader>();
-        for (File f : this.samFileList) {
-            SAMFileReader reader = initializeSAMFile(f);
-            if (reader == null) {
-                throw new SimpleDataSourceLoadException("SAMBAMDataSource: Unable to load file: " + f);
-            }
-            lst.add(reader);
-        }
-
-        // now merge the headers
-        SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(lst, SORT_ORDER);
-
-        // make a merging iterator for this record
-        MergingSamRecordIterator2 iter =  new MergingSamRecordIterator2(headerMerger);
-
-
-        // we do different things for locus and read modes
-        if (locusMode) {
-            iter.queryOverlapping(location.getContig(), (int) location.getStart(), (int) location.getStop());
-        } else {
-            iter.queryContained(location.getContig(), (int) location.getStart(), (int) location.getStop());
-        }
-
-        // return the iterator
-        return iter;
-    }
-
-    
-
-}