From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 28 Feb 2018 16:39:49 +0000 (+0000)
Subject: JAL-2909 Gaps at start of reads only from start of alignment window
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7798bd6a0235eb86769bb9987db735a3959ad031;p=jalview.git

JAL-2909 Gaps at start of reads only from start of alignment window
---

diff --git a/src/jalview/datamodel/CigarParser.java b/src/jalview/datamodel/CigarParser.java
index 95f1f2d..786896b 100644
--- 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())
@@ -335,7 +338,8 @@ 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());
 
diff --git a/src/jalview/io/BamFile.java b/src/jalview/io/BamFile.java
index 1aebbe9..277a61d 100644
--- a/src/jalview/io/BamFile.java
+++ b/src/jalview/io/BamFile.java
@@ -51,6 +51,9 @@ public class BamFile extends AlignFile
   // chromosome/contig to read
   private String chromosome = "";
 
+  // first position in alignment
+  private int alignmentStart = -1;
+
   /**
    * Creates a new BamFile object.
    */
@@ -122,13 +125,21 @@ public class BamFile extends AlignFile
       {
         SAMRecord rec = it.next();
 
+        // set the alignment start to be start of first read (we assume reads
+        // are sorted)
+        if (alignmentStart == -1)
+        {
+          alignmentStart = rec.getAlignmentStart();
+        }
+
         // make dataset sequence: start at 1, end at read length
         SequenceI seq = new Sequence(rec.getReadName(),
                 rec.getReadString().toLowerCase());
         seq.setStart(1);
         seq.setEnd(rec.getReadLength());
 
-        String newRead = parser.parseCigarToSequence(rec, insertions);
+        String newRead = parser.parseCigarToSequence(rec, insertions,
+                alignmentStart);
 
         // make alignment sequences
         SequenceI alsq = seq.deriveSequence();
diff --git a/test/jalview/datamodel/CigarParserTest.java b/test/jalview/datamodel/CigarParserTest.java
index 8df02e3..db3e198 100644
--- a/test/jalview/datamodel/CigarParserTest.java
+++ b/test/jalview/datamodel/CigarParserTest.java
@@ -89,7 +89,7 @@ public class CigarParserTest
     rec.setAlignmentStart(start);
 
     CigarParser cp = new CigarParser('-');
-    String bfresult = cp.parseCigarToSequence(rec, insertions);
+    String bfresult = cp.parseCigarToSequence(rec, insertions, 1);
 
     System.out.println(result);
     System.out.println(bfresult);