From c55aeeb5b277bf975a54ad59fb3173f88581cdfd Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 3 Dec 2010 12:38:10 +0000
Subject: [PATCH] implement next()
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15158 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/BCFReader.java | 199 +++++++++++-------
1 file changed, 121 insertions(+), 78 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/BCFReader.java b/uk/ac/sanger/artemis/components/variant/BCFReader.java
index c3f932f50..1c1f67e99 100644
--- a/uk/ac/sanger/artemis/components/variant/BCFReader.java
+++ b/uk/ac/sanger/artemis/components/variant/BCFReader.java
@@ -1,3 +1,26 @@
+/*
+ * created: 2010
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2010 Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or(at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ *
+ */
+
package uk.ac.sanger.artemis.components.variant;
import java.io.File;
@@ -16,60 +39,91 @@ import net.sf.samtools.util.BlockCompressedInputStream;
class BCFReader
{
public static final int TAD_LIDX_SHIFT = 13; // linear index shift
- private static Pattern formatPattern = Pattern.compile("[^0-9]+");
+ private static Pattern formatPattern = Pattern.compile("[^0-9]+");
+ private BlockCompressedInputStream is;
- public void query(File bcf, long offset, int beg, int end) throws IOException
+ public void query(File bcf, long offset) throws IOException
{
- BlockCompressedInputStream is = new BlockCompressedInputStream(bcf);
+ is = new BlockCompressedInputStream(bcf);
is.seek(offset);
-
- for(int i=0; i<7299; i++)
+ }
+
+
+ public VCFRecord next(int bid, int beg, int end) throws IOException
+ {
+ try
{
- int id = readInt(is);
- int pos = readInt(is)+1;
- float qual = readFloat(is);
- int slen = readInt(is);
- System.out.print("ID: "+id + " POS: "+pos + " QUAL: "+qual + " ");
- byte[] str = new byte[slen];
- is.read(str);
+ VCFRecord bcfRecord = readVCFRecord();
+ if(bcfRecord.pos >= beg && bcfRecord.pos <= end)
+ return bcfRecord;
+ else if(bcfRecord.pos < beg)
+ {
+ while( (bcfRecord = readVCFRecord()).pos <= beg )
+ {
+ if(bcfRecord.pos >= beg && bcfRecord.pos <= end)
+ return bcfRecord;
+ }
+ }
+ }
+ catch(Exception e)
+ {
+ if(is.read() != -1) // eof
+ e.printStackTrace();
+ }
+
+ return null;
+ }
+
+ private VCFRecord readVCFRecord() throws IOException
+ {
+ VCFRecord bcfRecord = new VCFRecord();
+ bcfRecord.seqID = readInt(is);
+ bcfRecord.pos = readInt(is)+1;
+ bcfRecord.quality = readFloat(is);
+
+ int slen = readInt(is);
+ byte[] str = new byte[slen];
+ is.read(str);
- String parts[] = getParts(str);
+ String parts[] = getParts(str);
+
+ bcfRecord.ref = parts[0];
+ bcfRecord.alt = parts[1];
+ String fmt = parts[parts.length-1];
+
+ if(formatPattern.matcher(fmt).matches())
+ {
+ bcfRecord.info = parts[parts.length-2];
+ bcfRecord.format = parts[parts.length-1];
- String ref = parts[0];
- String alt = parts[1];
- String fmt = parts[parts.length-1];
+ int nc = 3;
+ if(bcfRecord.alt.equals("."))
+ nc = 1;
- if(formatPattern.matcher(fmt).matches())
+ String fmts[] = bcfRecord.format.split(":");
+ for(int j=0; j<fmts.length; j++)
{
- String info = parts[parts.length-2];
- System.out.println(info+" "+fmt);
+ int nb = getByteSize(fmts[j],1,nc);
+ str = new byte[nb];
+ is.read(str);
- String format = parts[parts.length-1];
-
- int nc = 3;
- System.out.println("ALT:"+alt+" REF:"+ref);
- if(alt.equals("."))
- nc = 1;
-
- String fmts[] = format.split(":");
- for(int j=0; j<fmts.length; j++)
- {
- int nb = getByteSize(fmts[j],1,nc);
- str = new byte[nb];
- is.read(str);
-
- if(fmts[j].equals("GT"))
- System.out.println("nbytes = "+nb+" GT:"+getGTString(str[0]));
- else if(fmts[j].equals("PL"))
- System.out.println("nbytes = "+nb+" PL:"+getPLString(str, nc));
- else if(fmts[j].equals("DP")||fmts[j].equals("SP")||fmts[j].equals("GQ"))
- {
- System.out.println("nbytes = "+nb+" "+fmts[j]+":"+byteToInt(str[0]));
- }
-
- }
+ final String value;
+ if(fmts[j].equals("GT"))
+ value = getGTString(str[0]);
+ else if(fmts[j].equals("PL"))
+ value = getPLString(str, nc);
+ else if(fmts[j].equals("DP")||fmts[j].equals("SP")||fmts[j].equals("GQ"))
+ value = Integer.toString(byteToInt(str[0]));
+ else
+ value = "";
+ bcfRecord.data.put(fmts[j], value);
}
+
}
+ else
+ bcfRecord.info = parts[parts.length-1];
+
+ return bcfRecord;
}
/**
@@ -161,37 +215,34 @@ class BCFReader
return (int)(b & 0xFF);
}
- public static List<Index> load(File bcfIndex) throws IOException
+ protected static List<BCFIndex> loadIndex(File bcfIndex) throws IOException
{
FileInputStream fis = new FileInputStream(bcfIndex);
BlockCompressedInputStream is = new BlockCompressedInputStream(fis);
byte[] magic = new byte[4];
is.read(magic);
- System.out.println(new String(magic));
- int n = readInt(is);
+ if(!new String(magic).equals("BCI\4"))
+ System.err.println("Not a BCF index file:: "+new String(magic));
- List<Index> idx = new Vector<Index>(n);
+ int n = readInt(is);
+ List<BCFIndex> idx = new Vector<BCFIndex>(n);
for(int i=0; i<n; i++)
{
- Index idx2 = new Index();
+ BCFIndex idx2 = new BCFIndex();
idx2.n = readInt(is);
idx2.index2_offset = new long[idx2.n];
for(int j=0; j<idx2.n; j++)
- {
idx2.index2_offset[j] = readLong(is);
- }
-
- if(is.read() == -1)
- System.out.println("EOF");
+
idx.add(idx2);
}
return idx;
}
- public long queryIndex(List<Index> idx, int tid, int beg)
+ protected long queryIndex(List<BCFIndex> idx, int tid, int beg)
{
long min_off = -1;
if (beg < 0)
@@ -206,20 +257,20 @@ class BCFReader
return min_off;
}
- public static int readInt(final InputStream is) throws IOException {
+ protected static int readInt(final InputStream is) throws IOException {
byte[] buf = new byte[4];
is.read(buf);
return ByteBuffer.wrap(buf).order(ByteOrder.LITTLE_ENDIAN).getInt();
}
- public static float readFloat(final InputStream is) throws IOException {
+ protected static float readFloat(final InputStream is) throws IOException {
byte[] buf = new byte[4];
is.read(buf);
return ByteBuffer.wrap(buf).order(ByteOrder.LITTLE_ENDIAN).getFloat();
}
- public static long readLong(final InputStream is) throws IOException {
+ protected static long readLong(final InputStream is) throws IOException {
byte[] buf = new byte[8];
is.read(buf);
return ByteBuffer.wrap(buf).order(ByteOrder.LITTLE_ENDIAN).getLong();
@@ -229,25 +280,25 @@ class BCFReader
{
try
{
- List<Index> idx = load(new File(args[0]));
+ List<BCFIndex> idx = loadIndex(new File(args[0]));
- int sbeg;
- int send;
- if(args.length < 3)
- {
- sbeg = 326758;
- send = sbeg+1;
- }
- else
+ int sbeg = 0;
+ int send = Integer.MAX_VALUE;
+ if(args.length > 2)
{
sbeg = Integer.parseInt(args[2]);
send = Integer.parseInt(args[3]);
}
BCFReader reader = new BCFReader();
- long off = reader.queryIndex(idx, 0, sbeg);
- System.out.println(off);
- reader.query(new File(args[1]), off, sbeg, send);
+ int bid = 0;
+ long off = reader.queryIndex(idx, bid, sbeg);
+ reader.query(new File(args[1]), off);
+
+ VCFRecord bcfRecord;
+ while( (bcfRecord = reader.next(bid, sbeg, send)) != null )
+ System.out.println(bcfRecord.toString());
+
}
catch (IOException e)
{
@@ -257,16 +308,8 @@ class BCFReader
}
}
-class BCFRecord
-{
- int seqID;
- int pos;
- float quality;
- String info;
- String format;
-}
-class Index
+class BCFIndex
{
int n;
long index2_offset[];
--
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