From c3fff51bad7325789c84e9bdac09db4920dceee1 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 22 Feb 2011 14:41:38 +0000
Subject: [PATCH] optimise getParts()
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15578 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/BCFReader.java | 31 ++++++++++++++-----
1 file changed, 23 insertions(+), 8 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/BCFReader.java b/uk/ac/sanger/artemis/components/variant/BCFReader.java
index b746e9a5e..d68ca4bac 100644
--- a/uk/ac/sanger/artemis/components/variant/BCFReader.java
+++ b/uk/ac/sanger/artemis/components/variant/BCFReader.java
@@ -200,7 +200,7 @@ class BCFReader extends AbstractVCFReader
if(bcfRecord.getAlt().isNonVariant())
nc = 1;
- String fmts[] = bcfRecord.getFormat().split(":");
+ String fmts[] = VCFRecord.COLON_PATTERN.split( bcfRecord.getFormat() );
bcfRecord.setData( new String[nsamples][fmts.length] );
for(int j=0; j<nsamples; j++)
@@ -251,13 +251,28 @@ class BCFReader extends AbstractVCFReader
buff.append((char)b[i]);
}
- String parts[] = buff.toString().replace(" ", " ").split(" ");
- bcfRecord.setID( parts[0] );
- bcfRecord.setRef( parts[1] );
- bcfRecord.setAlt( parts[2] );
- bcfRecord.setFilter( parts[3] );
- bcfRecord.setInfo( parts[4] );
- bcfRecord.setFormat( parts[5] );
+ int ind = 0;
+ int lastInd = 0;
+ int i = 0;
+ while((ind = buff.indexOf(" ", ind)) > -1)
+ {
+ switch( i )
+ {
+ case 0: bcfRecord.setID(buff.substring(lastInd, ind)); break;
+ case 1: bcfRecord.setRef(buff.substring(lastInd, ind)); break;
+ case 2: bcfRecord.setAlt(buff.substring(lastInd, ind)); break;
+ case 3: bcfRecord.setFilter(buff.substring(lastInd, ind)); break;
+ case 4: bcfRecord.setInfo(buff.substring(lastInd, ind)); break;
+ case 5: bcfRecord.setFormat(buff.substring(lastInd, ind)); break;
+ default: return;
+ }
+
+ ind++;
+ if(ind < buff.length() && buff.charAt(ind) == ' ')
+ ind++;
+ lastInd = ind;
+ i++;
+ }
}
/**
--
GitLab