-set indel cleaning walkers to be in core package

-move Andrey's alignment utility classes to core


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1307 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/indels/CleanedReadInjector.java

@@ -1,10 +1,9 @@
-package org.broadinstitute.sting.playground.gatk.walkers.indels;
+package org.broadinstitute.sting.gatk.walkers.indels;
 
 import net.sf.samtools.SAMFileReader;
 import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.CloseableIterator;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.cmdLine.Argument;

java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelIntervalWalker.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.playground.gatk.walkers.indels;
+package org.broadinstitute.sting.gatk.walkers.indels;
 
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;

java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.playground.gatk.walkers.indels;
+package org.broadinstitute.sting.gatk.walkers.indels;
 
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.gatk.refdata.*;
@@ -9,7 +9,6 @@ import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.filters.Platform454Filter;
 import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
-import org.broadinstitute.sting.playground.indels.*;
 
 import net.sf.samtools.*;
 
@@ -338,7 +337,7 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
                     } catch (Exception e) {}
                 }
             } else {
-                logger.debug("CLEAN: " + cigarToString(bestConsensus.cigar) + " " + bestConsensus.str );
+                logger.debug("CLEAN: " + AlignmentUtils.cigarToString(bestConsensus.cigar) + " " + bestConsensus.str );
                 if ( indelOutput != null && bestConsensus.cigar.numCigarElements() > 1 ) {
                     // NOTE: indels are printed out in the format specified for the low-coverage pilot1
                     //  indel calls (tab-delimited): chr position size type sequence
@@ -421,7 +420,7 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
         // create the new consensus
         StringBuffer sb = new StringBuffer();
         sb.append(reference.substring(0, indexOnRef));
-        logger.debug("CIGAR = " + cigarToString(c));
+        logger.debug("CIGAR = " + AlignmentUtils.cigarToString(c));
 
         int indelCount = 0;
         int altIdx = 0;
@@ -673,7 +672,7 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
         int difference = 0; // we can move indel 'difference' bases left
         final int indel_length = ce2.getLength();
 
-        String indelString = null; // inserted or deleted sequence
+        String indelString; // inserted or deleted sequence
         int period = 0; // period of the inserted/deleted sequence
         int indelIndexOnRef = refIndex+ce1.getLength() ; // position of the indel on the REF (first deleted base or first base after insertion)
         int indelIndexOnRead = readIndex+ce1.getLength(); // position of the indel on the READ (first insterted base, of first base after deletion)
@@ -753,7 +752,7 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
             //            if ( ce2.getLength() >=2 )
             //                System.out.println("  REALIGNED TO:\n"+AlignmentUtils.alignmentToString(newCigar,readSeq,refSeq,refIndex,readIndex)+"\n");
 
-            logger.debug("Realigning indel: " + cigarToString(cigar) + " to " + cigarToString(newCigar));
+            logger.debug("Realigning indel: " + AlignmentUtils.cigarToString(cigar) + " to " + AlignmentUtils.cigarToString(newCigar));
             cigar = newCigar;
 
         }
@@ -794,7 +793,7 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
             if ( getCigar().equals(cigar) )
                 return false;
 
-            String str = cigarToString(cigar);
+            String str = AlignmentUtils.cigarToString(cigar);
             if ( !str.contains("D") && !str.contains("I") )
                 return false;
 
@@ -992,23 +991,4 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
         reads.add(r8);
         clean(reads, reference, GenomeLocParser.createGenomeLoc(0,0));
     }
-
-    public static String cigarToString(Cigar cig) {
-        if ( cig == null )
-            return "null";
-
-        StringBuilder b = new StringBuilder();
-
-        for ( int i = 0 ; i < cig.numCigarElements() ; i++ ) {
-            char c='?';
-            switch ( cig.getCigarElement(i).getOperator() ) {            
-                case M : c = 'M'; break;
-                case D : c = 'D'; break;
-                case I : c = 'I'; break;
-            }
-            b.append(cig.getCigarElement(i).getLength());
-            b.append(c);
-        }
-        return b.toString(); 
-    }
 }

java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java

@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.playground.gatk.walkers.indels;
+package org.broadinstitute.sting.gatk.walkers.indels;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;

java/src/org/broadinstitute/sting/gatk/walkers/indels/MismatchIntervalWalker.java

@@ -1,5 +1,5 @@
 
-package org.broadinstitute.sting.playground.gatk.walkers.indels;
+package org.broadinstitute.sting.gatk.walkers.indels;
 
 import net.sf.samtools.*;
 import org.broadinstitute.sting.gatk.refdata.*;

java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java

@@ -1,5 +1,5 @@
 
-package org.broadinstitute.sting.playground.gatk.walkers.indels;
+package org.broadinstitute.sting.gatk.walkers.indels;
 
 import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.LocusContext;

java/src/org/broadinstitute/sting/utils/AlignmentUtils.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.playground.indels;
+package org.broadinstitute.sting.utils;
 
 import net.sf.samtools.CigarOperator;
 import net.sf.samtools.SAMRecord;
@@ -6,7 +6,6 @@ import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.picard.reference.ReferenceSequence;
 import org.broadinstitute.sting.playground.utils.CountedObject;
-import org.broadinstitute.sting.utils.*;
 
 import java.util.*;
 
@@ -176,103 +175,6 @@ public class AlignmentUtils {
     	return n;
     }
 
-    
-    /** Reads through the alignment cigar and returns all indels found in the alignment as a collection
-     * of Indel objects.
-     * @param c alignment cigar
-     * @param start alignment start. NOTE: if cigar starts with clipped bases (S), alignment start position should be set after them according to SAM format specification.
-     * @return
-     */
-    public static Collection<Indel> extractIndels(final Cigar c, final int start) {
-        //
-        // firstpos,lastpos span of the indel will be interpreted as follows:
-        // any alignment that ends strictly before firstpos or starts strictly after lastpos
-        // on the *reference* (not inclusive!) does not overlap with an indel; in the case of
-        // insertion it will result in firstpos > lastpos!
-        //         lastpos
-        //         |   firstpos
-        //         |   |
-        //         v   v
-        // ---------III----- Ref  Insertion: bases I are not in the ref; any alignment that starts
-        //                        after lastpos or ends before firstpos *on the reference*
-        //                        is completely over the reference bases to the right or to
-        //                        the left, respectively, of the insertion site
-        //
-        //      firstpos
-        //      | lastpos
-        //      | |
-        //      v v
-        //------------------ Ref   Deletion: any alignment that ends before firstpos or starts after lastpos
-        // -----DDD--- alignment   on the reference does not overlap with the deletion
-        int runninglength = start; // position on the original reference; start = alignment start position
-
-        List<Indel> indels = new ArrayList<Indel>(4);
-
-        if ( c.numCigarElements() <= 1 ) return indels; // most of the reads have no indels, save a few cycles by returning early
-
-        for ( int i = 0 ; i < c.numCigarElements() ; i++ ) {
-
-            final CigarElement ce = c.getCigarElement(i);
-            Indel curr_indel = null;
-
-            switch(ce.getOperator()) {
-            case I:
-                    curr_indel = new Indel(runninglength, ce.getLength(), Indel.IndelType.I);
-                    if ( i == 0 ) System.out.println("WARNING: Indel at start of the read");
-                    if ( i == c.numCigarElements() - 1) System.out.println("WARNING: Indel at end of the read");
-                    break;
-            case D: curr_indel = new Indel(runninglength, ce.getLength(), Indel.IndelType.D);
-                    if ( i == 0 ) System.out.println("WARNING: Indel at start of the read");
-                    if ( i == c.numCigarElements() - 1) System.out.println("WARNING: Indel at end of the read");
-                    runninglength += ce.getLength();
-                    break;
-            case M: runninglength += ce.getLength(); break; // advance along the gapless block in the alignment
-            case H:
-            case S: break; // just skip hard and soft-clipped bases; according to SAM format specification, alignment start position on the reference
-            	                       // points to where the actually aligned (not clipped) bases go, so we do not need to increment reference position here
-            default :
-                throw new IllegalArgumentException("Unexpected operator in cigar string: "+ce.getOperator());
-            }
-
-            if ( curr_indel == null ) continue; // element was not an indel, go grab next element...
-
-            indels.add(curr_indel); // this is a new indel. Add it.
-        } // end for loop over all alignment cigar elements
-
-        return indels;
-    } // end extractIndels() method
-
-    /** Reads through the alignment specified in the record and returns all indels found in the alignment as a collection
-     * of Indel objects. If read is not mapped, silently returns an empty collection.
-     * @param r
-     * @return
-     */
-    public static Collection<Indel> extractIndels(SAMRecord r) {
-        if ( r.getReadUnmappedFlag() ) return new ArrayList<Indel>();
-        return extractIndels(r.getCigar(), r.getAlignmentStart());
-    }
-
-    /** Extracts indels from the specified record (@see #extractIndels()) and updates the provided tree object.
-     * Multiple occurences of the same indel (i.e. with support from multiple reads) will be grouped together
-     * in one counted object held by the set.
-     *
-     * @param r
-     * @param t
-     */
-    public static void collectAndCountIndels(SAMRecord r, TreeSet<CountedObject<Indel> > t) {
-        Collection<Indel> indels = AlignmentUtils.extractIndels(r);
-        for ( Indel ind : indels ) {
-            CountedObject<Indel> ci = new CountedObject<Indel>(ind);
-            CountedObject<Indel> found = t.floor(ci);
-//            CountedObject<Indel> found2 = t.ceiling(ci);
-
-            if ( ci.equals( found ) ) found.increment(); // we did find our indel, advance the counter
-            else t.add(ci); // this is a new indel. Add it.
-
-        }
-
-    }
-
     public static String toString(Cigar cig) {
         StringBuilder b = new StringBuilder();
 
@@ -294,6 +196,25 @@ public class AlignmentUtils {
         return alignmentToString( cigar, seq, ref, posOnRef, 0 );
     }
 
+    public static String cigarToString(Cigar cig) {
+        if ( cig == null )
+            return "null";
+
+        StringBuilder b = new StringBuilder();
+
+        for ( int i = 0 ; i < cig.numCigarElements() ; i++ ) {
+            char c='?';
+            switch ( cig.getCigarElement(i).getOperator() ) {
+                case M : c = 'M'; break;
+                case D : c = 'D'; break;
+                case I : c = 'I'; break;
+            }
+            b.append(cig.getCigarElement(i).getLength());
+            b.append(c);
+        }
+        return b.toString();
+    }
+
     public static String alignmentToString(final Cigar cigar,final  String seq, final String ref, final int posOnRef, final int posOnRead ) {
         int readPos = posOnRead;
         int refPos = posOnRef;

java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java

@@ -1,6 +1,5 @@
-package org.broadinstitute.sting.playground.indels;
+package org.broadinstitute.sting.utils;
 
-import org.broadinstitute.sting.utils.PrimitivePair;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
 import net.sf.samtools.Cigar;