From ca8b62e56942ffa55ca16db50f7bf680b5a33588 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Mon, 6 Feb 2012 16:26:37 +0000
Subject: [PATCH] add reference sequence
---
.../artemis/components/variant/IOUtils.java | 91 ++++++++++++-------
1 file changed, 59 insertions(+), 32 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index 80ec4dff8..4a7b8dba0 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -34,7 +34,7 @@ import java.io.InputStream;
import java.io.PrintWriter;
import java.io.Writer;
import java.net.URL;
-import java.util.Hashtable;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Vector;
@@ -181,12 +181,13 @@ class IOUtils
final EntryGroup entryGroup = vcfView.getEntryGroup();
final int length = entryGroup.getSequenceLength();
final Bases bases = entryGroup.getBases();
- FeatureVector features = entryGroup.getAllFeatures();
-
+ final FeatureVector features = entryGroup.getAllFeatures();
+
final String name = entryGroup.getActiveEntries().elementAt(0).getName();
final File newfile = new File(
getBaseDirectoryFromEntry(entryGroup.getActiveEntries().elementAt(0)),
name);
+
try
{
final File f = getFile(newfile.getAbsolutePath(), 1, ".fasta", null);
@@ -197,39 +198,44 @@ class IOUtils
for (int i = 0; i < vcfView.getVcfReaders().length; i++)
ntotalSamples += vcfView.getVcfReaders()[i].getNumberOfSamples();
- final Writer[] writer = new Writer[ntotalSamples];
- final File[] tmpFiles = new File[ntotalSamples];
+ final Writer[] writer = new Writer[ntotalSamples+1];
+ final File[] tmpFiles = new File[ntotalSamples+1];
for (int i = 0; i < vcfView.getVcfReaders().length; i++)
{
final String names[] = vcfView.getVcfReaders()[i].sampleNames;
for(int j=0; j<names.length; j++)
{
- tmpFiles[i] = File.createTempFile(names[j].replaceAll("[/\\:]", "_"), "art");
- writer[i] = new FileWriter( tmpFiles[i] );
- writer[i].write(">"+names[j]);
+ tmpFiles[i+j] = File.createTempFile(names[j].replaceAll("[/\\:]", "_"), "art");
+ writer[i+j] = new FileWriter( tmpFiles[i+j] );
+ writer[i+j].write(">"+names[j]);
}
}
+
+ // include reference bases
+ tmpFiles[ntotalSamples] = File.createTempFile("ref", "art");
+ writer[ntotalSamples] = new FileWriter( tmpFiles[ntotalSamples] );
+ writer[ntotalSamples].write(">reference");
- int MAX_BASE_CHUNK = (10000/ntotalSamples)*SEQUENCE_LINE_BASE_COUNT;
- //System.out.println("MAX_BASE_CHUNK "+MAX_BASE_CHUNK);
- final Hashtable<Integer, VCFRecord> records[] = new Hashtable[MAX_BASE_CHUNK];
+ final int MAX_BASE_CHUNK = (10000/ntotalSamples)*SEQUENCE_LINE_BASE_COUNT;
+ final HashMap<Integer, VCFRecord> records[] = new HashMap[MAX_BASE_CHUNK];
int baseCount = 0;
- // write variant sites to temp files
+ // write variant sites to tmp files
for(int i=0; i<length; i+=MAX_BASE_CHUNK)
{
- int end = i+MAX_BASE_CHUNK;
int start = i+1;
+ int end = i+MAX_BASE_CHUNK;
if(end > length)
end = length;
storeVCFRecords(vcfView, records, start, end);
- baseCount = writeVariants(vcfView, records, writer, features, ntotalSamples, start, end, baseCount);
+ baseCount = writeVariants(vcfView, records, writer, features,
+ ntotalSamples, start, end, bases, baseCount);
}
- for(int i=0; i<ntotalSamples; i++)
+ for(int i=0; i<writer.length; i++)
writer[i].close();
// concatenate the single fasta files into a multiple fasta file
@@ -249,6 +255,10 @@ class IOUtils
{
e.printStackTrace();
}
+ catch (OutOfRangeException e)
+ {
+ e.printStackTrace();
+ }
}
/**
@@ -260,13 +270,13 @@ class IOUtils
* @throws IOException
*/
private static void storeVCFRecords(final VCFview vcfView,
- final Hashtable<Integer, VCFRecord> records[],
+ final HashMap<Integer, VCFRecord> records[],
final int start,
final int end) throws IOException
{
for (int i = 0; i < vcfView.getVcfReaders().length; i++)
- records[i] = new Hashtable<Integer, VCFRecord> ();
+ records[i] = new HashMap<Integer, VCFRecord> ();
for (int i = 0; i < vcfView.getVcfReaders().length; i++)
{
@@ -298,7 +308,7 @@ class IOUtils
}
}
- private static void loadRecords(Hashtable<Integer, VCFRecord> records,
+ private static void loadRecords(HashMap<Integer, VCFRecord> records,
final AbstractVCFReader reader,
final String contig,
final int start,
@@ -309,25 +319,43 @@ class IOUtils
while((record = reader.getNextRecord(contig, start, end)) != null)
{
if(records == null)
- records = new Hashtable<Integer, VCFRecord> ();
+ records = new HashMap<Integer, VCFRecord> ();
records.put(record.getPos()+offset, record);
}
}
+ /**
+ * Write variant positions.
+ * @param vcfView
+ * @param records
+ * @param writer
+ * @param features
+ * @param ntotalSamples
+ * @param start
+ * @param end
+ * @param bases
+ * @param bc
+ * @return
+ * @throws IOException
+ * @throws OutOfRangeException
+ */
private static int writeVariants(final VCFview vcfView,
- final Hashtable<Integer, VCFRecord> records[],
- final Writer writer[],
- final FeatureVector features,
- final int ntotalSamples,
- final int start,
- final int end,
- int bc) throws IOException
+ final HashMap<Integer, VCFRecord> records[],
+ final Writer writer[],
+ final FeatureVector features,
+ final int ntotalSamples,
+ final int start,
+ final int end,
+ final Bases bases,
+ int bc) throws IOException, OutOfRangeException
{
+ final char basesC[] = bases.getSubSequenceC(new Range(start, end), Bases.FORWARD);
for (int i = start; i < end; i++)
{
int basePosition = i;
int thisSample = 0;
- final String[] thisBase = new String[ntotalSamples];
+ final String[] thisBase = new String[ntotalSamples+1];
+
boolean seenSNP = false;
int insertionLength = 0;
@@ -387,6 +415,9 @@ class IOUtils
if(seenSNP)
{
+ // look-up reference base
+ thisBase[ntotalSamples] = String.valueOf( basesC[i-start] );
+
int remainder = 0;
for(int j=0; j<thisBase.length; j++)
{
@@ -395,10 +426,6 @@ class IOUtils
for(int k=0; k<thisBase[j].length(); k++)
{
remainder = (bc+k)%SEQUENCE_LINE_BASE_COUNT;
-
- /*if(j==0 && k==0 && bc>3299 && bc<3365)
- System.out.println("HERE "+thisBase[j]+" "+bc+" "+basePosition+" "+remainder);*/
-
if(remainder == 0)
writer[j].write(System.getProperty("line.separator"));
writer[j].write(thisBase[j].charAt(k));
@@ -430,7 +457,7 @@ class IOUtils
}
}
}
-
+
if(insertionLength > 0)
bc+=insertionLength;
else
--
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