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JAL-2909 add sequence feature for quality
author
Jim Procter
<jprocter@issues.jalview.org>
Fri, 2 Mar 2018 10:35:28 +0000
(10:35 +0000)
committer
Jim Procter
<jprocter@issues.jalview.org>
Fri, 2 Mar 2018 10:35:28 +0000
(10:35 +0000)
src/jalview/io/BamFile.java
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diff --git
a/src/jalview/io/BamFile.java
b/src/jalview/io/BamFile.java
index
10e2d0e
..
c8bac62
100644
(file)
--- a/
src/jalview/io/BamFile.java
+++ b/
src/jalview/io/BamFile.java
@@
-22,12
+22,14
@@
package jalview.io;
import jalview.datamodel.CigarParser;
import jalview.datamodel.Sequence;
import jalview.datamodel.CigarParser;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import jalview.datamodel.SequenceI;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
+import java.util.PrimitiveIterator.OfInt;
import java.util.SortedMap;
import htsjdk.samtools.SAMRecord;
import java.util.SortedMap;
import htsjdk.samtools.SAMRecord;
@@
-137,7
+139,15
@@
public class BamFile extends AlignFile
rec.getReadString().toLowerCase());
seq.setStart(1);
seq.setEnd(rec.getReadLength());
rec.getReadString().toLowerCase());
seq.setStart(1);
seq.setEnd(rec.getReadLength());
-
+ 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,
alignmentStart, seq);
String newRead = parser.parseCigarToSequence(rec, insertions,
alignmentStart, seq);