changes to use Picard

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11714 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/alignment/Read.java

-/* Read
- *
- * created: 2009
- *
- * This file is part of Artemis
- *
- * Copyright(C) 2009  Genome Research Limited
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or(at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
- *
- */
-package uk.ac.sanger.artemis.components.alignment;
-
-class Read
-{
-  String qname; // query name
-  int flag;     // bitwise flag
-  String rname; // reference name
-  int pos;      // leftmost coordinate
-  short mapq;   // MAPping Quality
-  String cigar; // extended CIGAR string
-  String mrnm;  // Mate Reference sequence NaMe; Ò=Ó if the same as rname
-  int mpos;     // leftmost Mate POSition
-  int isize;    // inferred Insert SIZE
-  String seq;   // query SEQuence; Ò=Ó for a match to the reference; n/N/. for ambiguity
-  
-  public String toString()
-  {
-    return qname+"\t"+
-           flag+"\t"+
-           rname+"\t"+
-           pos+"\t"+
-           mapq+"\t"+
-           cigar+"\t"+
-           mrnm+"\t"+
-           mpos+"\t"+
-           isize+"\t"+
-           seq;
-  }
-}
\ No newline at end of file

uk/ac/sanger/artemis/components/alignment/RunSamTools.java

@@ -26,6 +26,8 @@ package uk.ac.sanger.artemis.components.alignment;
 import java.io.*;
 import java.util.List;
 
+import net.sf.samtools.SAMRecord;
+
 /**
 * Used to run an samtools process this reads stdout and 
 * stderr in separate threads.
@@ -36,7 +38,7 @@ public class RunSamTools
   /** running process */
   private Process p;
   /** standard out */
-  private List<Read> readsInView;
+  private List<SAMRecord> readsInView;
   /** standard error */
   private StringBuffer stderr = new StringBuffer();
   private StringBuffer stdout = new StringBuffer();
@@ -57,7 +59,7 @@ public class RunSamTools
   public RunSamTools(String cmd[], 
                      String[] envp,
                      File project,
-                     List<Read> readsInView)
+                     List<SAMRecord> readsInView)
   {
     //this.project = project;
     this.readsInView = readsInView;
@@ -156,17 +158,18 @@ public class RunSamTools
         {
           String fields[] = line.split("\t");
 
-          Read pread = new Read();
-          pread.qname = fields[0];
-          pread.flag  = Integer.parseInt(fields[1]);
-          pread.rname = fields[2];
-          pread.pos   = Integer.parseInt(fields[3]);
-          pread.mapq  = Short.parseShort(fields[4]);
-          pread.cigar = fields[5];
-          pread.mrnm  = fields[6];
-          pread.mpos  = Integer.parseInt(fields[7]);
-          pread.isize = Integer.parseInt(fields[8]);
-          pread.seq   = fields[9];
+          SAMRecord pread = new SAMRecord(null);
+          pread.setReadName(fields[0]);
+          pread.setFlags(Integer.parseInt(fields[1]));
+          pread.setReferenceName(fields[2]);
+          pread.setAlignmentStart(Integer.parseInt(fields[3]));
+          pread.setMappingQuality(Integer.parseInt(fields[4]));
+          pread.setCigarString(fields[5]);
+          pread.setMateReferenceName(fields[6]);
+          pread.setMateAlignmentStart( Integer.parseInt(fields[7]));
+          pread.setInferredInsertSize(Integer.parseInt(fields[8]));
+          pread.setReadString(fields[9]);
+          
           readsInView.add(pread);
         }
         else