From 36cbfe1c98674d4f1358c8a66182128c47edf635 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 8 Feb 2012 09:01:23 +0000
Subject: [PATCH] fixes for writing out variant sites
---
.../artemis/components/variant/IOUtils.java | 32 ++++++++++++-------
1 file changed, 21 insertions(+), 11 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index 4a7b8dba0..0a2765e03 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -179,7 +179,7 @@ class IOUtils
protected static void exportVariantFasta(final VCFview vcfView)
{
final EntryGroup entryGroup = vcfView.getEntryGroup();
- final int length = entryGroup.getSequenceLength();
+ int length = entryGroup.getSequenceLength();
final Bases bases = entryGroup.getBases();
final FeatureVector features = entryGroup.getAllFeatures();
@@ -223,6 +223,7 @@ class IOUtils
int baseCount = 0;
// write variant sites to tmp files
+ //length = 2172095;
for(int i=0; i<length; i+=MAX_BASE_CHUNK)
{
int start = i+1;
@@ -352,13 +353,12 @@ class IOUtils
final char basesC[] = bases.getSubSequenceC(new Range(start, end), Bases.FORWARD);
for (int i = start; i < end; i++)
{
- int basePosition = i;
- int thisSample = 0;
+ int thisSample = 0;
final String[] thisBase = new String[ntotalSamples+1];
boolean seenSNP = false;
int insertionLength = 0;
-
+
// loop over each VCF file
for (int j = 0; j < vcfView.getVcfReaders().length; j++)
{
@@ -368,13 +368,14 @@ class IOUtils
if(record == null)
continue;
+
boolean vcf_v4 = reader.isVcf_v4();
int nsamples = reader.getNumberOfSamples();
// loop over each sample
for(int k=0; k<nsamples; k++)
{
// look at each type of variant
- if(vcfView.showVariant(record, features, basePosition, reader, k, j) )
+ if(vcfView.showVariant(record, features, i, reader, k, j) )
{
if(record.getAlt().isDeletion(vcf_v4))
{
@@ -402,13 +403,21 @@ class IOUtils
thisBase[thisSample] = ".";
else
{
- thisBase[thisSample] = record.getAlt().toString();
- seenSNP = true;
+ if(record.getAlt().toString().length() > 1 &&
+ record.getAlt().toString().length() == record.getRef().length() )
+ {
+ thisBase[thisSample] = record.getAlt().toString();
+ seenSNP = true;
+
+ if(thisBase[ntotalSamples] == null ||
+ thisBase[ntotalSamples].length() < record.getRef().length())
+ thisBase[ntotalSamples] = record.getRef();
+ }
}
}
else
thisBase[thisSample] = "N"; // filtered out
-
+
thisSample++;
}
}
@@ -416,11 +425,12 @@ class IOUtils
if(seenSNP)
{
// look-up reference base
- thisBase[ntotalSamples] = String.valueOf( basesC[i-start] );
+ if(thisBase[ntotalSamples] == null)
+ thisBase[ntotalSamples] = String.valueOf( basesC[i-start] );
int remainder = 0;
for(int j=0; j<thisBase.length; j++)
- {
+ {
if(thisBase[j] != null)
{
for(int k=0; k<thisBase[j].length(); k++)
@@ -455,7 +465,7 @@ class IOUtils
writer[j].write(System.getProperty("line.separator"));
writer[j].write("-");
}
- }
+ }
}
if(insertionLength > 0)
--
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