From e54718558eac4a009adfa4901b636ccb25e4478d Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 12 May 2011 10:23:30 +0000
Subject: [PATCH] allow for SP type change in bcftoools
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16072 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/BCFReader.java | 20 ++++++++++++++++---
1 file changed, 17 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/BCFReader.java b/uk/ac/sanger/artemis/components/variant/BCFReader.java
index d4114fb91..54da10e24 100644
--- a/uk/ac/sanger/artemis/components/variant/BCFReader.java
+++ b/uk/ac/sanger/artemis/components/variant/BCFReader.java
@@ -49,6 +49,8 @@ class BCFReader extends AbstractVCFReader
private int nsamples;
private String metaData;
private String fileName;
+
+ private boolean longSP = true;
private static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(BCFReader.class);
@@ -106,7 +108,14 @@ class BCFReader extends AbstractVCFReader
if(bcfRecord.getPos() >= beg && bcfRecord.getPos() <= end)
return bcfRecord;
}
- }
+ }
+ catch(ArrayIndexOutOfBoundsException ae)
+ {
+ if(longSP)
+ longSP = false;
+ else
+ throw ae;
+ }
catch(Exception e)
{
if(is.read() != -1) // eof
@@ -213,7 +222,7 @@ class BCFReader extends AbstractVCFReader
int n_alleles = bcfRecord.getAlt().getNumAlleles();
int nc = (int) (n_alleles * ((float)(((float)n_alleles+1.f)/2.f)));
- if(bcfRecord.getAlt().isNonVariant())
+ if(bcfRecord.getAlt().isNonVariant() && bcfRecord.getAlt().equals("."))
nc = 1;
String fmts[] = VCFRecord.COLON_PATTERN.split( bcfRecord.getFormat() );
@@ -325,7 +334,12 @@ class BCFReader extends AbstractVCFReader
else if(tag.equals("PL")) // Phred-scaled likelihood
return nsamples*nc; // uint8_t[n*x]
else if(tag.equals("SP")) //
- return nsamples; // uint8_t[n]
+ {
+ if(longSP) // type changed in bcftools
+ return 4*nsamples; // uint32_t[n]
+ else
+ return nsamples; // uint8_t[n]
+ }
else // misc
return 4*nsamples; // uint32_t+char*
}
--
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