From fdd123fe162eb8e4948379ab92b087bf5f0a7e8e Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 14 May 2009 16:53:07 +0000
Subject: [PATCH] A parser the raw Illumina data.  Allows one to arbitrarily
 jump from one tile to another.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@703 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/secondarybase/IlluminaParser.java   | 160 ++++++++++++++++++
 1 file changed, 160 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/secondarybase/IlluminaParser.java

diff --git a/java/src/org/broadinstitute/sting/secondarybase/IlluminaParser.java b/java/src/org/broadinstitute/sting/secondarybase/IlluminaParser.java
new file mode 100755
index 000000000..224f568c2
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/secondarybase/IlluminaParser.java
@@ -0,0 +1,160 @@
+package org.broadinstitute.sting.secondarybase;
+
+import org.broadinstitute.sting.utils.StingException;
+
+import java.io.File;
+import java.io.FilenameFilter;
+import java.io.Closeable;
+import java.io.IOException;
+import java.util.regex.Pattern;
+import java.util.regex.Matcher;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.Iterator;
+
+import edu.mit.broad.picard.util.PasteParser;
+import edu.mit.broad.picard.util.BasicTextFileParser;
+
+public class IlluminaParser implements Iterator<RawRead>, Iterable<RawRead>, Closeable {
+    private File bustardDir;
+    private File firecrestDir;
+    private int lane;
+    private int cycleBegin;
+    private int cycleEnd;
+
+    private File[] intfiles;
+    private File[] seqfiles;
+    private File[] prbfiles;
+
+    private int currentTileIndex;
+    private PasteParser currentTileParser;
+
+    private boolean iterating = false;
+
+    public IlluminaParser(File bustardDir, int lane, int cycleBegin, int cycleEnd) {
+        this.bustardDir = bustardDir;
+        this.firecrestDir = bustardDir.getParentFile();
+        this.lane = lane;
+        this.cycleBegin = cycleBegin;
+        this.cycleEnd = cycleEnd;
+
+        initializeParser();
+    }
+
+    public IlluminaParser(File bustardDir, File firecrestDir, int lane, int cycleBegin, int cycleEnd) {
+        this.bustardDir = bustardDir;
+        this.firecrestDir = firecrestDir;
+        this.lane = lane;
+        this.cycleBegin = cycleBegin;
+        this.cycleEnd = cycleEnd;
+        
+        initializeParser();
+    }
+
+    private void initializeParser() {
+        intfiles = firecrestDir.listFiles(getFilenameFilter("int"));
+        seqfiles = bustardDir.listFiles(getFilenameFilter("seq"));
+        prbfiles = bustardDir.listFiles(getFilenameFilter("prb"));
+
+        if (intfiles.length != seqfiles.length || intfiles.length != prbfiles.length || seqfiles.length != prbfiles.length) {
+            throw new StingException(
+                String.format("File list lengths are unequal (int:%d, seq:%d, prb:%d)",
+                              intfiles.length,
+                              seqfiles.length,
+                              prbfiles.length)
+            );
+        }
+
+        Arrays.sort(intfiles, getTileSortingComparator());
+        Arrays.sort(seqfiles, getTileSortingComparator());
+        Arrays.sort(prbfiles, getTileSortingComparator());
+
+        iterator();
+
+        // Todo: put some more consistency checks here
+
+    }
+
+    private FilenameFilter getFilenameFilter(final String suffix) {
+        return new FilenameFilter() {
+            public boolean accept(File file, String s) {
+                Pattern pseq = Pattern.compile(String.format("s_%d_\\d+_%s\\.txt(?!.+old.+)(\\.gz)?", lane, suffix));
+                Matcher mseq = pseq.matcher(s);
+
+                return mseq.find();
+            }
+        };
+    }
+
+    private Comparator<File> getTileSortingComparator() {
+        return new Comparator<File>() {
+            public int compare(File file1, File file2) {
+                Pattern ptile = Pattern.compile(String.format("s_%d_(\\d+)_", lane));
+
+                Matcher mtile1 = ptile.matcher(file1.getName());
+                Matcher mtile2 = ptile.matcher(file2.getName());
+
+                if (mtile1.find() && mtile2.find()) {
+                    int tile1 = Integer.valueOf(mtile1.group(1));
+                    int tile2 = Integer.valueOf(mtile2.group(1));
+
+                    if (tile1 < tile2) { return -1; }
+                    else if (tile1 > tile2) { return 1; }
+
+                    return 0;
+                }
+
+                throw new StingException("Tile filenames ('" + file1.getName() + "' or '" + file2.getName() + "') did not match against regexp pattern ('" + ptile.pattern() + "')");
+            }
+        };
+    }
+
+    public int numTiles() { return intfiles.length; }
+
+    public boolean seekToTile(int tile) {
+        if (tile < intfiles.length - 1) {
+            currentTileIndex = tile - 1;
+
+            BasicTextFileParser intparser = new BasicTextFileParser(true, intfiles[currentTileIndex]);
+            BasicTextFileParser seqparser = new BasicTextFileParser(true, seqfiles[currentTileIndex]);
+            BasicTextFileParser prbparser = new BasicTextFileParser(true, prbfiles[currentTileIndex]);
+
+            currentTileParser = new PasteParser(intparser, seqparser, prbparser);
+
+            return true;
+        }
+
+        return false;
+    }
+
+    public boolean hasNext() {
+        return (currentTileParser.hasNext() || seekToTile(currentTileIndex + 1));
+    }
+
+    public RawRead next() {
+        if (hasNext()) {
+            return new RawRead(currentTileParser.next(), cycleBegin, cycleEnd);
+        }
+
+        return null;
+    }
+
+    public void remove() {
+        throw new UnsupportedOperationException("IlluminaParser.remove() method is not supported.");
+    }
+
+    public Iterator<RawRead> iterator() {
+        if (iterating) {
+            throw new IllegalStateException("IlluminaParser.iterator() method can only be called once, before the first call to IlluminaParser.hasNext()");
+        }
+
+        seekToTile(1);
+        iterating = true;
+        
+        return this;
+    }
+
+    public void close() {
+        currentTileParser.close();
+    }
+}