From 1476ddc3ee0191f3590925a6824fdccb27f3b17f Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 7 Dec 2010 12:18:38 +0000
Subject: [PATCH] check chr in next() and catch exception in looking up offset
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15191 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/BCFReader.java | 44 +++++++++++++++----
.../artemis/components/variant/VCFview.java | 14 ++----
2 files changed, 39 insertions(+), 19 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/BCFReader.java b/uk/ac/sanger/artemis/components/variant/BCFReader.java
index 577afe8a0..8414edf3a 100644
--- a/uk/ac/sanger/artemis/components/variant/BCFReader.java
+++ b/uk/ac/sanger/artemis/components/variant/BCFReader.java
@@ -67,17 +67,23 @@ class BCFReader extends AbstractVCFReader
is.seek(off);
}
- protected VCFRecord next(int beg, int end) throws IOException
+ protected VCFRecord next(String chr, int beg, int end) throws IOException
{
try
{
VCFRecord bcfRecord = readVCFRecord();
+ if(chr != null && !bcfRecord.getChrom().equals(chr))
+ return null;
+
if(bcfRecord.getPos() >= beg && bcfRecord.getPos() <= end)
return bcfRecord;
else if(bcfRecord.getPos() < beg)
{
while( (bcfRecord = readVCFRecord()).getPos() <= beg )
{
+ if(chr != null && !bcfRecord.getChrom().equals(chr))
+ return null;
+
if(bcfRecord.getPos() >= beg && bcfRecord.getPos() <= end)
return bcfRecord;
}
@@ -335,7 +341,7 @@ class BCFReader extends AbstractVCFReader
int send = Integer.MAX_VALUE;
VCFRecord record;
- while( (record = reader.next(sbeg, send)) != null)
+ while( (record = reader.next(null, sbeg, send)) != null)
writer.write(record.toString()+"\n");
writer.close();
}
@@ -386,9 +392,15 @@ class BCFReader extends AbstractVCFReader
long offset[] = idx.get(tid).index2_offset;
int i;
- for(i = beg>>TAD_LIDX_SHIFT; i < idx.get(tid).n && offset[i] == 0; ++i);
- min_off = (i == idx.get(tid).n)? offset[idx.get(tid).n-1] : offset[i];
-
+ try
+ {
+ for(i = beg>>TAD_LIDX_SHIFT; i < idx.get(tid).n && offset[i] == 0; ++i);
+ min_off = (i == idx.get(tid).n)? offset[idx.get(tid).n-1] : offset[i];
+ }
+ catch(ArrayIndexOutOfBoundsException e)
+ {
+ return offset[offset.length-1];
+ }
return min_off;
}
@@ -403,22 +415,36 @@ class BCFReader extends AbstractVCFReader
{
int sbeg = 0;
int send = Integer.MAX_VALUE;
+ String chr = null;
if(args.length > 1)
{
- sbeg = Integer.parseInt(args[1]);
- send = Integer.parseInt(args[2]);
+ String parts[] = args[1].split(":");
+ chr = parts[0];
+
+ String rgn[] = parts[1].split("-");
+ sbeg = Integer.parseInt(rgn[0]);
+ send = Integer.parseInt(rgn[1]);
}
BCFReader reader = new BCFReader(new File(args[0]));
int bid = 0;
+ if(chr != null)
+ bid = reader.getSeqIndex(chr);
long off = reader.queryIndex(bid, sbeg);
reader.seek(off);
System.out.println(reader.headerToString());
VCFRecord bcfRecord;
- while( (bcfRecord = reader.next(sbeg, send)) != null )
- System.out.println(bcfRecord.toString());
+ while( (bcfRecord = reader.next(chr, sbeg, send)) != null )
+ {
+ System.out.println(bcfRecord.getChrom());
+ if(chr != null && bcfRecord.getChrom().equals(chr))
+ System.out.println(bcfRecord.toString());
+ else
+ break;
+ }
+
reader.close();
}
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index 51a1313d0..d410be34e 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -785,11 +785,8 @@ public class VCFview extends JPanel
bcfReader.seek(off);
VCFRecord bcfRecord;
- while( (bcfRecord = bcfReader.next(sbeg, send)) != null )
- {
- if(bcfRecord.getChrom().equals(chr))
- drawVariantCall(g, bcfRecord, start, i, pixPerBase, features);
- }
+ while( (bcfRecord = bcfReader.next(chr, sbeg, send)) != null )
+ drawVariantCall(g, bcfRecord, start, i, pixPerBase, features);
}
catch (IOException e)
{
@@ -1210,11 +1207,8 @@ public class VCFview extends JPanel
{
bcfReader.seek(off);
VCFRecord bcfRecord;
- while( (bcfRecord = bcfReader.next(sbeg, send)) != null )
- {
- if(bcfRecord.getChrom().equals(chr))
- isMouseOver(mousePoint, bcfRecord, features, i, start, pixPerBase);
- }
+ while( (bcfRecord = bcfReader.next(chr, sbeg, send)) != null )
+ isMouseOver(mousePoint, bcfRecord, features, i, start, pixPerBase);
}
catch (IOException e)
{
--
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