JAL-2909 Updated tests

[jalview.git] / src / jalview / datamodel / CigarParser.java

diff --git a/src/jalview/datamodel/CigarParser.java b/src/jalview/datamodel/CigarParser.java
index 95f1f2d..0abe9bf 100644 (file)
--- a/src/jalview/datamodel/CigarParser.java
+++ b/src/jalview/datamodel/CigarParser.java
@@ -27,10 +27,13 @@ public class CigarParser
    *          the SAM record for the read
    * @param insertions
    *          a map of inserted positions and lengths
+   * @param alignmentStart
+   *          start of alignment to be used as offset when padding reads with
+   *          gaps
    * @return string representing read with gaps, clipping etc applied
    */
   public String parseCigarToSequence(SAMRecord rec,
-          SortedMap<Integer, Integer> insertions)
+          SortedMap<Integer, Integer> insertions, int alignmentStart)
   {
     StringBuilder newRead = new StringBuilder();
     Iterator<CigarElement> it = rec.getCigar().getCigarElements()
@@ -42,11 +45,11 @@ public class CigarParser
     // pad with spaces before read
     // first count gaps needed to pad to reference position
     // NB position is 1-based so number of gaps = pos-1
-    int gaps = rec.getStart() - 1; // rec.getUnclippedStart() - 1;
+    int gaps = rec.getStart() - alignmentStart;
+
     // now count gaps to pad for insertions in other reads
     int insertCount = countInsertionsBeforeRead(rec, insertions);
     addGaps(newRead, gaps + insertCount);
-    // addGaps(newTrimmedRead, gaps + insertCount);
 
     int lastinserts = 0;
     while (it.hasNext())
@@ -65,11 +68,12 @@ public class CigarParser
         {
           // ERROR
           int pos = rec.getStart() + refnext;
-          System.out.println("Insertion not added to seqInserts: " + pos);
+          System.out.println(
+                  "Read " + rec.getReadName() + " has an insertion at "
+                          + pos + " which is not in seqInserts");
         }
         else
         {
-
           // we just inserted something
           // remove these inserts now - should be very first entry
           int count = seqInserts.get(rec.getStart() + refnext);
@@ -191,11 +195,12 @@ public class CigarParser
     StringBuilder newRead = new StringBuilder();
     String read = rec.getReadString();
 
-    int nextPos = next;
+    int nextPos = next; // location of next position in read
     while (nextPos < next + length)
     {
-      int insertPos = next + length;
-      int insertLen = 0;
+      int insertPos = next + length; // location of next insert in read (or end
+                                     // of read)
+      int insertLen = 0; // no of gaps to insert after insertPos
       if (it.hasNext())
       {
         // account for sequence already having insertion
@@ -217,6 +222,11 @@ public class CigarParser
         {
           insertPos = rec.getReadPositionAtReferencePosition(key) - 1;
         }
+        else
+        {
+          insertPos = nextPos; // bugfix - trigger by override + insertions in
+                               // same M stretch
+        }
       }
       newRead.append(read.substring(nextPos, insertPos));
       nextPos = insertPos;
@@ -261,7 +271,7 @@ public class CigarParser
       SAMRecord rec = it.next();
       Iterator<CigarElement> cit = rec.getCigar().getCigarElements()
               .iterator();
-      int next = 0;
+      int next = 1;
       while (cit.hasNext())
       {
         CigarElement el = cit.next();
@@ -269,12 +279,11 @@ public class CigarParser
         {
         case I:
           // add to insertions list, and move along the read
-          // location is 1 past the current position of next
-          // (note if we try to retrieve +1 position from reference by calling
-          // getReferencePositionAtReadPosition(next+1) we get 0 because it's an
-          // insertion!)
-          int refLocation = rec.getReferencePositionAtReadPosition(next)
-                  + 1;
+          // location is the start of next CIGAR segment
+          // because getReferencePositionAtReadPosition returns 0 for read
+          // positions which are not in the reference (like insertions)
+          int refLocation = rec.getReferencePositionAtReadPosition(
+                  next + el.getLength());
 
           // if there's already an insertion at this location, keep the longest
           // insertion; if there's no insertion keep this one
@@ -335,7 +344,8 @@ public class CigarParser
     int gaps = 0;
 
     // add in any insertion gaps before read
-    // TODO start point should be start of alignment not 0
+    // although we only need to get the submap from alignmentStart, there won't
+    // be any insertions before that so we can just start at 0
     SortedMap<Integer, Integer> seqInserts = inserts.subMap(0,
             rec.getStart());