X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBamFile.java;h=8d55c537661b2ac3442cf60e6b82a6af09425d14;hb=429bbdae3d5229ec1b92ec59f4b5a25bcfcf13f8;hp=1aebbe9519e9500ad9d819e731116b8998465620;hpb=9289ad58228571a63fdf54ef720603a590d58adc;p=jalview.git

diff --git a/src/jalview/io/BamFile.java b/src/jalview/io/BamFile.java
index 1aebbe9..8d55c53 100644
--- a/src/jalview/io/BamFile.java
+++ b/src/jalview/io/BamFile.java
@@ -21,18 +21,24 @@
 package jalview.io;
 
 import jalview.datamodel.CigarParser;
+import jalview.datamodel.Range;
 import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 
 import java.io.File;
 import java.io.IOException;
+import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
+import java.util.PrimitiveIterator.OfInt;
 import java.util.SortedMap;
 
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SAMRecordIterator;
 import htsjdk.samtools.SAMSequenceRecord;
+import htsjdk.samtools.SamInputResource;
 import htsjdk.samtools.SamReader;
 import htsjdk.samtools.SamReaderFactory;
 import htsjdk.samtools.ValidationStringency;
@@ -51,6 +57,9 @@ 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.
    */
@@ -89,13 +98,24 @@ public class BamFile extends AlignFile
   public BamFile(FileParse source) throws IOException
   {
     super(true, source);
+    parseSuffix();
     final SamReaderFactory factory = SamReaderFactory.makeDefault()
             .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS,
                     SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS)
             .validationStringency(ValidationStringency.SILENT);
 
     // File-based bam
-    fileReader = factory.open(source.inFile);
+    if (source.getDataSourceType() == DataSourceType.FILE)
+    {
+      fileReader = factory.open(source.inFile);
+    }
+    else
+    {
+      // locate index ?
+      String index = source.getDataName() + ".bai";
+      fileReader = factory.open(SamInputResource.of(source.getDataName())
+              .index(new URL(index)));
+    }
   }
   
   @Override
@@ -105,6 +125,44 @@ public class BamFile extends AlignFile
     return null;
   }
 
+  private StringBuilder insertRefSeq(
+          SortedMap<Integer, Integer> insertions, Range xtent)
+  {
+    StringBuilder refseq = new StringBuilder();
+    int inserted = 0;
+    for (int p = xtent.start; p < xtent.end; p++)
+    {
+      refseq.append('N');
+    }
+    for (Map.Entry<Integer, Integer> insert : insertions.entrySet())
+    {
+      int inspos = insert.getKey() - xtent.start + inserted;
+      if (inspos < 0)
+      {
+        System.out.println("Ignoring -ve insert position " + insert.getKey()
+                + " of " + insert.getValue() +
+                " (alpos: " + inspos + ")");
+        inspos = 0;
+        // continue;
+      }
+      for (int i = 0, j = insert.getValue(); i < j; i++)
+      {
+        inserted++;
+        refseq.insert(inspos, '-');
+      }
+    }
+    return refseq;
+  }
+
+  private void padRef(SequenceI ref, CigarParser cig)
+  { // pad to column
+    int padding = cig.firstAlColumn - ref.findIndex(cig.firstRposCol);
+    System.out.println("Padding " + padding + " to move refseq position "
+            + cig.firstRposCol + " to " + cig.firstAlColumn + "col.");
+
+    ref.insertCharAt(0, padding, '-');
+  }
+
   @Override
   public void parse()
   {
@@ -114,21 +172,60 @@ public class BamFile extends AlignFile
       SAMRecordIterator it = fileReader.query(chromosome, start, end,
               false);
       CigarParser parser = new CigarParser('-');
-      SortedMap<Integer, Integer> insertions = parser.getInsertions(it);
+      Range[] xtent = new Range[] { new Range(start, end) };
+      SortedMap<Integer, Integer> insertions[] = parser.getInsertions(it,
+              xtent);
       it.close();
 
+      SequenceI refSeq = new Sequence("chr:" + chromosome,
+              insertRefSeq(insertions[0], xtent[0])
+                      .toString());
+
+      refSeq.setStart(xtent[0].start);
+      refSeq.setEnd(xtent[0].end);
+      SequenceI revRefSeq = new Sequence("rev:chr:" + chromosome,
+              insertRefSeq(insertions[1], xtent[0])
+                      .toString());
+      revRefSeq.setStart(xtent[0].start);
+      revRefSeq.setEnd(xtent[0].end);
+
+      // Hack to move the seqs along
+      padRef(refSeq, parser);
+      padRef(revRefSeq, parser);
+
       it = fileReader.query(chromosome, start, end, false);
+
+      ArrayList<SequenceI> fwd = new ArrayList(), rev = new ArrayList();
       while (it.hasNext())
       {
         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(),
+        SequenceI seq = new Sequence(
+                "" + (rec.getReadNegativeStrandFlag() ? "rev:" : "")
+                        + rec.getReadName(),
                 rec.getReadString().toLowerCase());
         seq.setStart(1);
         seq.setEnd(rec.getReadLength());
-
-        String newRead = parser.parseCigarToSequence(rec, insertions);
+        OfInt q = rec.getBaseQualityString().chars()
+                .iterator();
+        int p = seq.getStart();
+        while (q.hasNext())
+        {
+          seq.addSequenceFeature(new SequenceFeature("QUALITY", "", p, p,
+                  (float) q.next() - ' ', "bamfile"));
+          p++;
+        }
+        String newRead = parser.parseCigarToSequence(rec,
+                insertions[rec.getReadNegativeStrandFlag() ? 1 : 0],
+                alignmentStart, seq);
 
         // make alignment sequences
         SequenceI alsq = seq.deriveSequence();
@@ -136,7 +233,28 @@ public class BamFile extends AlignFile
 
         // set start relative to soft clip; assume end is set by Sequence code
         alsq.setStart(rec.getStart() - rec.getUnclippedStart() + 1);
-        seqs.add(alsq);
+        if (rec.getReadNegativeStrandFlag())
+        {
+          rev.add(alsq);
+        }
+        else
+        {
+          fwd.add(alsq);
+        }
+      }
+      // Add forward
+      if (fwd.size() > 0)
+      {
+        seqs.add(refSeq); // FIXME needs to be optional, and properly padded
+        seqs.addAll(fwd);
+        fwd.clear();
+      }
+      // and reverse strand reads.
+      if (rev.size() > 0)
+      {
+        seqs.add(revRefSeq); // FIXME needs to be optional and properly padded
+        seqs.addAll(rev);
+        rev.clear();
       }
     }
   }
@@ -166,5 +284,39 @@ public class BamFile extends AlignFile
     chromosome = chr;
     start = s;
     end = e;
+    suffix = chromosome + ":" + start + "-" + end;
+  }
+
+  public boolean parseSuffix()
+  {
+    if (suffix == null)
+    {
+      return false;
+    }
+    int csep = suffix.indexOf(":");
+    int rsep = suffix.indexOf("-", csep);
+    if (csep < 0 || rsep < 0 || suffix.length() - rsep <= 1)
+    {
+      return false;
+    }
+    String chr, p1, p2;
+    chr = suffix.substring(0, csep);
+    p1 = suffix.substring(csep + 1, rsep);
+    p2 = suffix.substring(rsep + 1);
+    int cstart, cend;
+    try
+    {
+      cstart = Integer.parseInt(p1);
+      cend = Integer.parseInt(p2);
+    } catch (Exception e)
+    {
+      warningMessage = (warningMessage == null ? "" : warningMessage + "\n")
+              + "Couldn't parse range from " + suffix;
+      return false;
+    }
+    chromosome = chr;
+    start = cstart;
+    end = cend;
+    return true;
   }
 }