From 077be9ea9e7006362af3c3f70191c1f51eacde2c Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 11 Jan 2012 14:59:22 +0000
Subject: [PATCH] optimise getParts()
---
.../artemis/components/variant/BCFReader.java | 46 ++++++++++++++++++-
1 file changed, 45 insertions(+), 1 deletion(-)
diff --git a/uk/ac/sanger/artemis/components/variant/BCFReader.java b/uk/ac/sanger/artemis/components/variant/BCFReader.java
index 38bd15820..42c1d2484 100644
--- a/uk/ac/sanger/artemis/components/variant/BCFReader.java
+++ b/uk/ac/sanger/artemis/components/variant/BCFReader.java
@@ -298,6 +298,50 @@ class BCFReader extends AbstractVCFReader
* @return
*/
private void getParts(final byte[] b, final VCFRecord bcfRecord)
+ {
+ int index = 0;
+ final StringBuilder buff = new StringBuilder();
+
+ for(int i=0; i<b.length; i++)
+ {
+ if(b[i] == 0 && (i == 0 || b[i-1] == 0) )
+ {
+ switch( index )
+ {
+ case 0: bcfRecord.setID("."); break;
+ case 1: bcfRecord.setRef("."); break;
+ case 2: bcfRecord.setAlt(":"); break; // this looks like a non-variant site
+ case 3: bcfRecord.setFilter("."); break;
+ case 4: bcfRecord.setInfo("."); break;
+ case 5: bcfRecord.setFormat("."); break;
+ default: return;
+ }
+ index++;
+ }
+ if(b[i] == 0)
+ continue;
+
+ buff.setLength(0);
+ buff.append((char)b[i]);
+ while(i < b.length-1 && b[i+1] != 0)
+ buff.append((char)b[++i]);
+
+ switch( index )
+ {
+ case 0: bcfRecord.setID(buff.toString()); break;
+ case 1: bcfRecord.setRef(buff.toString()); break;
+ case 2: bcfRecord.setAlt(buff.toString()); break;
+ case 3: bcfRecord.setFilter(buff.toString()); break;
+ case 4: bcfRecord.setInfo(buff.toString()); break;
+ case 5: bcfRecord.setFormat(buff.toString()); break;
+ default: return;
+ }
+ index++;
+ }
+ }
+
+
+ /*private void getParts(final byte[] b, final VCFRecord bcfRecord)
{
final StringBuilder buff = new StringBuilder();
for(int i=0; i<b.length; i++)
@@ -336,7 +380,7 @@ class BCFReader extends AbstractVCFReader
lastInd = ind;
i++;
}
- }
+ }*/
/**
* DP uint16 t[n] Read depth
--
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