diff --git a/uk/ac/sanger/artemis/components/variant/BCFReader.java b/uk/ac/sanger/artemis/components/variant/BCFReader.java
index 5a770b76720f40e7ea3646e7290e4706866664a4..2f5f2e3ed6605e8659fa13a141c0939f3ebc514c 100644
--- a/uk/ac/sanger/artemis/components/variant/BCFReader.java
+++ b/uk/ac/sanger/artemis/components/variant/BCFReader.java
@@ -26,6 +26,7 @@ package uk.ac.sanger.artemis.components.variant;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
+import java.io.Writer;
import java.util.List;
import java.util.Vector;
import java.util.regex.Pattern;
@@ -66,21 +67,21 @@ class BCFReader extends AbstractVCFReader
is.seek(off);
}
- protected VCFRecord next(int bid, int beg, int end) throws IOException
+ protected VCFRecord next(int beg, int end) throws IOException
{
try
{
VCFRecord bcfRecord = readVCFRecord();
- if(bcfRecord.pos >= beg && bcfRecord.pos <= end)
+ if(bcfRecord.getPos() >= beg && bcfRecord.getPos() <= end)
return bcfRecord;
- else if(bcfRecord.pos < beg)
+ else if(bcfRecord.getPos() < beg)
{
- while( (bcfRecord = readVCFRecord()).pos <= beg )
+ while( (bcfRecord = readVCFRecord()).getPos() <= beg )
{
- if(bcfRecord.pos >= beg && bcfRecord.pos <= end)
+ if(bcfRecord.getPos() >= beg && bcfRecord.getPos() <= end)
return bcfRecord;
}
- if(bcfRecord.pos >= beg && bcfRecord.pos <= end)
+ if(bcfRecord.getPos() >= beg && bcfRecord.getPos() <= end)
return bcfRecord;
}
}
@@ -173,9 +174,9 @@ class BCFReader extends AbstractVCFReader
private VCFRecord readVCFRecord() throws IOException
{
VCFRecord bcfRecord = new VCFRecord();
- bcfRecord.chrom = seqNames[readInt(is)];
- bcfRecord.pos = readInt(is)+1;
- bcfRecord.quality = readFloat(is);
+ bcfRecord.setChrom( seqNames[readInt(is)] );
+ bcfRecord.setPos ( readInt(is)+1 );
+ bcfRecord.setQuality( readFloat(is) );
int slen = readInt(is);
byte[] str = new byte[slen];
@@ -183,16 +184,16 @@ class BCFReader extends AbstractVCFReader
getParts(str, bcfRecord);
- if(formatPattern.matcher(bcfRecord.format).matches())
+ if(formatPattern.matcher(bcfRecord.getFormat()).matches())
{
int n_alleles = bcfRecord.getNumAlleles();
int nc = (int) (n_alleles * ((float)(((float)n_alleles+1.f)/2.f)));
- if(bcfRecord.alt.equals("."))
+ if(bcfRecord.getAlt().equals("."))
nc = 1;
- String fmts[] = bcfRecord.format.split(":");
- bcfRecord.data = new String[nsamples][fmts.length];
+ String fmts[] = bcfRecord.getFormat().split(":");
+ bcfRecord.setData( new String[nsamples][fmts.length] );
for(int j=0; j<nsamples; j++)
{
@@ -212,7 +213,7 @@ class BCFReader extends AbstractVCFReader
else
value = "";
- bcfRecord.data[j][k] = value;
+ bcfRecord.getData()[j][k] = value;
}
}
@@ -255,12 +256,12 @@ class BCFReader extends AbstractVCFReader
String parts[] = buff.toString().replace(" ", " ").split(" ");
- bcfRecord.ID = parts[0];
- bcfRecord.ref = parts[1];
- bcfRecord.alt = parts[2];
- bcfRecord.filter = parts[3];
- bcfRecord.info = parts[4];
- bcfRecord.format = parts[5];
+ bcfRecord.setID( parts[0] );
+ bcfRecord.setRef( parts[1] );
+ bcfRecord.setAlt( parts[2] );
+ bcfRecord.setFilter( parts[3] );
+ bcfRecord.setInfo( parts[4] );
+ bcfRecord.setFormat( parts[5] );
}
/**
@@ -325,6 +326,20 @@ class BCFReader extends AbstractVCFReader
return (int)(b & 0xFF);
}
+ protected static void writeVCF(Writer writer, String vcfFileName) throws IOException
+ {
+ BCFReader reader = new BCFReader(new File(vcfFileName));
+ writer.write( reader.headerToString()+"\n" );
+
+ int sbeg = 0;
+ int send = Integer.MAX_VALUE;
+ VCFRecord record;
+
+ while( (record = reader.next(sbeg, send)) != null)
+ writer.write(record.toString()+"\n");
+ writer.close();
+ }
+
protected List<BCFIndex> loadIndex() throws IOException
{
BlockCompressedInputStream is = new BlockCompressedInputStream(indexFileStream);
@@ -402,7 +417,7 @@ class BCFReader extends AbstractVCFReader
System.out.println(reader.headerToString());
VCFRecord bcfRecord;
- while( (bcfRecord = reader.next(bid, sbeg, send)) != null )
+ while( (bcfRecord = reader.next(sbeg, send)) != null )
System.out.println(bcfRecord.toString());
reader.close();
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index a9970bf9aa46dcefd55a4445d4a42b8d8be711cd..78ea19e7f437e3776dc38e45de03f7519e946582 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -533,7 +533,7 @@ public class VCFview extends JPanel
{
VCFview.this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
IOUtils.export(entryGroup, vcfFiles, VCFview.this);
- VCFview.this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
+ VCFview.this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
}
});
popup.add(exportVCF);
@@ -776,8 +776,11 @@ public class VCFview extends JPanel
bcfReader.seek(off);
VCFRecord bcfRecord;
- while( (bcfRecord = bcfReader.next(bid, sbeg, send)) != null )
- drawVariantCall(g, bcfRecord, start, i, pixPerBase, features);
+ while( (bcfRecord = bcfReader.next(sbeg, send)) != null )
+ {
+ if(bcfRecord.getChrom().equals(chr))
+ drawVariantCall(g, bcfRecord, start, i, pixPerBase, features);
+ }
}
catch (IOException e)
{
@@ -991,30 +994,30 @@ public class VCFview extends JPanel
//String parts[] = line.split("\\t");
//String parts[] = tabPattern.split(line, 0);
- int basePosition = record.pos + getSequenceOffset(record.chrom);
+ int basePosition = record.getPos() + getSequenceOffset(record.getChrom());
- if( !showVariant(record.ref, record.alt, features, basePosition, record.quality) )
+ if( !showVariant(record.getRef(), record.getAlt(), features, basePosition, record.getQuality()) )
return;
int pos[] = getScreenPosition(basePosition, pixPerBase, start, index);
- if(isDeletion(record.ref, record.alt))
+ if(isDeletion(record.getRef(), record.getAlt()))
g.setColor(Color.gray);
- else if(isInsertion(record.ref, record.alt))
+ else if(isInsertion(record.getRef(), record.getAlt()))
g.setColor(Color.yellow);
- else if(record.alt.equals("C") && record.ref.length() == 1)
+ else if(record.getAlt().equals("C") && record.getRef().length() == 1)
g.setColor(Color.red);
- else if(record.alt.equals("A") && record.ref.length() == 1)
+ else if(record.getAlt().equals("A") && record.getRef().length() == 1)
g.setColor(Color.green);
- else if(record.alt.equals("G") && record.ref.length() == 1)
+ else if(record.getAlt().equals("G") && record.getRef().length() == 1)
g.setColor(Color.blue);
- else if(record.alt.equals("T") && record.ref.length() == 1)
+ else if(record.getAlt().equals("T") && record.getRef().length() == 1)
g.setColor(Color.black);
- else if(record.alt.equals(".") && record.ref.length() == 1)
+ else if(record.getAlt().equals(".") && record.getRef().length() == 1)
g.setColor(Color.magenta);
else
{
- Matcher m = multiAllelePattern.matcher(record.alt);
+ Matcher m = multiAllelePattern.matcher(record.getAlt());
if(m.matches())
{
g.setColor(Color.orange);
@@ -1191,8 +1194,11 @@ public class VCFview extends JPanel
{
bcfReader.seek(off);
VCFRecord bcfRecord;
- while( (bcfRecord = bcfReader.next(bid, sbeg, send)) != null )
- isMouseOver(mousePoint, bcfRecord, features, i, start, pixPerBase);
+ while( (bcfRecord = bcfReader.next(sbeg, send)) != null )
+ {
+ if(bcfRecord.getChrom().equals(chr))
+ isMouseOver(mousePoint, bcfRecord, features, i, start, pixPerBase);
+ }
}
catch (IOException e)
{
@@ -1228,9 +1234,9 @@ public class VCFview extends JPanel
int i,
int start, float pixPerBase)
{
- int basePosition = record.pos + getSequenceOffset(record.chrom);
+ int basePosition = record.getPos() + getSequenceOffset(record.getChrom());
- if( !showVariant(record.ref, record.alt, features, basePosition, record.quality) )
+ if( !showVariant(record.getRef(), record.getAlt(), features, basePosition, record.getQuality()) )
return;
int pos[] = getScreenPosition(basePosition, pixPerBase, start, i);