From f63be8a93eb5963c3e501b3c4ea5045c1180c700 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 17 Feb 2011 10:46:11 +0000
Subject: [PATCH] fixes to getSeqsVariation()
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15552 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/IOUtils.java | 48 +++++++++++++------
1 file changed, 34 insertions(+), 14 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index 5c806a7e3..344350998 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -45,6 +45,7 @@ import uk.ac.sanger.artemis.components.MessageDialog;
import uk.ac.sanger.artemis.components.StickyFileChooser;
import uk.ac.sanger.artemis.components.variant.BCFReader.BCFReaderIterator;
import uk.ac.sanger.artemis.io.Key;
+import uk.ac.sanger.artemis.sequence.Bases;
import net.sf.samtools.util.BlockCompressedInputStream;
@@ -182,7 +183,7 @@ class IOUtils
int sbeg = seg.getRawRange().getStart();
int send = seg.getRawRange().getEnd();
String segBases = seg.getBases();
-
+
if (vcfReaders[i] instanceof BCFReader)
{
BCFReaderIterator it = ((BCFReader) vcfReaders[i]).query(chr, sbeg, send);
@@ -198,7 +199,7 @@ class IOUtils
final String product = f.getProductString();
header.append( (product == null ? "undefined product" : product) );
header.append(" ").append(f.getWriteRange());
-
+
writeSequence(writer, header.toString(), buff.toString());
}
@@ -230,23 +231,30 @@ class IOUtils
{
int position = vcfRecord.getPos()-sbeg;
if(!isFwd)
- position = bases.length()-position;
+ position = bases.length()-position-1;
if(position > bases.length())
return bases;
+ else if(position < 0)
+ return bases;
+ if(position < bases.length()-1 && bases.charAt(position) == '-')
+ return bases;
+
StringBuffer buff = new StringBuffer();
- if(isFwd)
- buff.append(bases.substring(0,position));
- else if(position > 0)
- buff.append(bases.substring(0,position-1));
+ buff.append(bases.substring(0,position));
if(vcfRecord.getAlt().isDeletion(vcf_v4))
{
int ndel = vcfRecord.getAlt().getNumberOfDeletions(vcf_v4);
+
+ if(isFwd)
+ position+=ndel;
+ else
+ buff.delete(position-ndel+1, position);
+
for(int i=0; i<ndel; i++)
buff.append("-");
- position+=ndel;
}
else if(vcfRecord.getAlt().isInsertion(vcf_v4))
{
@@ -256,16 +264,28 @@ class IOUtils
{
}
- else if(vcfRecord.getAlt().isNonVariant()) // non-variant SNP
- buff.append(vcfRecord.getRef());
+ else if(vcfRecord.getAlt().isNonVariant()) // non-variant
+ {
+ if(isFwd)
+ buff.append(vcfRecord.getRef().toUpperCase());
+ else
+ buff.append(Bases.complement(vcfRecord.getRef()).toUpperCase());
+ }
else
- buff.append(vcfRecord.getAlt().toString().toLowerCase()); // SNP
+ {
+ String alt = vcfRecord.getAlt().toString().toLowerCase(); // SNP
+ if(isFwd)
+ buff.append(alt);
+ else
+ buff.append(Bases.complement(alt));
+ }
if(isFwd && position < bases.length())
buff.append(bases.substring(position+1));
- else
- buff.append(bases.substring(position));
-
+ else if(!isFwd)
+ {
+ buff.append(bases.substring(position+1));
+ }
return buff.toString();
}
--
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