From 8cb16a1d45d3dc2ed6d817f0710e2bfcad56b49a Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 16 Jun 2010 02:13:08 +0000
Subject: [PATCH] a) Cleanup, remove -input argument from
 BeagleOutputToVCFWalker since it's not needed. b) Added back old Beagle ROD
 to maintain backward compatibility (does anyone even use this???)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3563 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/BeagleROD.java         | 112 ++++++++++++++++++
 .../gatk/walkers/BeagleOutputToVCFWalker.java |   3 -
 2 files changed, 112 insertions(+), 3 deletions(-)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/refdata/BeagleROD.java

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/BeagleROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/BeagleROD.java
new file mode 100755
index 000000000..e1bd47f00
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/BeagleROD.java
@@ -0,0 +1,112 @@
+/*
+ * 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 org.broadinstitute.sting.gatk.refdata;
+
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.text.XReadLines;
+
+import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+import java.io.IOException;
+import java.io.File;
+import java.io.FileNotFoundException;
+
+public class BeagleROD extends BasicReferenceOrderedDatum {
+    GenomeLoc loc;
+    List<String> sampleNames = null;
+    Map<String, List<String>> sampleGenotypes = new HashMap<String, List<String>>();
+
+    public BeagleROD(String name) {
+        super(name);
+    }
+
+    public String toString() { return "BeagleRod"; }
+
+    public String delimiterRegex() {
+        return " ";
+    }
+
+    public GenomeLoc getLocation() {
+        return loc;
+    }
+
+    public List<String> getSampleNames() {
+        return sampleNames;
+    }
+
+    public Map<String, List<String>> getGenotypes() {
+        return sampleGenotypes;
+    }
+
+    public Object initialize(final File source) throws FileNotFoundException {
+        String firstLine = new XReadLines(source).next();
+        String[] parts = firstLine.split(" ");
+        if ( parts[0].equals("I") ) {
+            // I id NA12891 NA12891 NA12892 NA12892
+            sampleNames = Arrays.asList(parts).subList(2, parts.length);
+            return sampleNames;
+        } else {
+            throw new IllegalStateException("Beagle file " + source + " doesn't have required header line I");
+        }
+    }
+
+    private static Pattern MARKER_PATTERN = Pattern.compile("c(.+)_p([0-9]+)");
+
+    public static GenomeLoc parseMarkerName(String markerName) {
+        Matcher m = MARKER_PATTERN.matcher(markerName);
+        if ( m.matches() ) {
+            String contig = m.group(1);
+            long start = Long.valueOf(m.group(2));
+            return GenomeLocParser.createGenomeLoc(contig, start, start);
+        } else {
+            throw new IllegalArgumentException("Malformatted family structure string: " + markerName + " required format is mom+dad=child");
+        }
+    }
+
+    public boolean parseLine(final Object header, final String[] parts) throws IOException {
+        //System.out.printf("Parsing beagle parts=%s header=%s%n", parts, header);
+        List<String> sampleNames = (List<String>)header;
+
+        if ( parts.length == 0 || ! parts[0].equals("M") )
+            return false;
+        else {
+            loc = parseMarkerName(parts[1]);
+
+            for ( int i = 2; i < parts.length; i++ ) {
+                String sampleName = sampleNames.get(i-2);
+                if ( ! sampleGenotypes.containsKey(sampleName) ) {
+                    sampleGenotypes.put(sampleName, new ArrayList<String>());
+                }
+
+                sampleGenotypes.get(sampleName).add(parts[i]);
+            }
+
+            return true;
+        }
+    }
+}
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
index 1d6ccfe7d..cf5a8f61d 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
@@ -61,9 +61,6 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
 
     private VCFWriter vcfWriter;
 
-    @Argument(fullName="input_prefix", shortName="input", doc="The prefix added to input Beagle files gprobs, r2, ...", required=true)
-    private String INPUT_PREFIX = "beagle";
-
     @Argument(fullName="output_file", shortName="output", doc="VCF file to which output should be written", required=true)
     private String OUTPUT_FILE = null;