From 9cc478de5574f3dc2d6183f13f9a74278aa22beb Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Sat, 4 Dec 2010 10:08:22 +0000
Subject: [PATCH] assign contents of VCFRecord in getParts()
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15162 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/BCFReader.java | 54 ++++++++++---------
1 file changed, 28 insertions(+), 26 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/BCFReader.java b/uk/ac/sanger/artemis/components/variant/BCFReader.java
index e8ebc4bb1..6998a27c8 100644
--- a/uk/ac/sanger/artemis/components/variant/BCFReader.java
+++ b/uk/ac/sanger/artemis/components/variant/BCFReader.java
@@ -178,18 +178,10 @@ class BCFReader
byte[] str = new byte[slen];
is.read(str);
- String parts[] = getParts(str);
+ getParts(str, bcfRecord);
- bcfRecord.ID = parts[0];
- bcfRecord.ref = parts[1];
- bcfRecord.alt = parts[2];
- String fmt = parts[parts.length-1];
-
- if(formatPattern.matcher(fmt).matches())
- {
- bcfRecord.info = parts[parts.length-2];
- bcfRecord.format = parts[parts.length-1];
-
+ if(formatPattern.matcher(bcfRecord.format).matches())
+ {
int nc = 3;
if(bcfRecord.alt.equals("."))
nc = 1;
@@ -214,40 +206,50 @@ class BCFReader
}
}
- else
- bcfRecord.info = parts[parts.length-1];
return bcfRecord;
}
/**
- * Make a string from the byte array. Expanding NULL padding.
+ * Make a string from the byte array (expanding NULL padding) to
+ * determine the parts:- ID+REF+ALT+FILTER+INFO+FORMAT.
* @param b
* @return
*/
- private String[] getParts(byte[] b)
+ private void getParts(byte[] b, VCFRecord bcfRecord)
{
StringBuffer buff = new StringBuffer();
+
for(int i=0; i<b.length; i++)
{
- if(i == 0 && b[i] == 0)
- {
- buff.append(". ");
- continue;
- }
-
if(b[i] == 0)
{
- if(i > 0 && b[i-1] == 0 && b[i+1] == 0)
- buff.append(".");
+ if(i == 0)
+ {
+ buff.append(". ");
+ continue;
+ }
+
+ if(b[i-1] == 0 || (i < b.length-1 && b[i+1] == 0))
+ {
+ i++;
+ buff.append(" . ");
+ }
else
buff.append(" ");
+ continue;
}
- else
- buff.append((char)b[i]);
+ buff.append((char)b[i]);
}
- return buff.toString().split(" ");
+ String parts[] = buff.toString().replace(" ", " ").split(" ");
+
+ bcfRecord.ID = parts[0];
+ bcfRecord.ref = parts[1];
+ bcfRecord.alt = parts[2];
+ bcfRecord.filter = parts[3];
+ bcfRecord.info = parts[4];
+ bcfRecord.format = parts[5];
}
/**
--
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