From c8d8eb7aa209d71a271537010c3573d43c1f1e24 Mon Sep 17 00:00:00 2001
From: James Stalker <jws@sanger.ac.uk>
Date: Wed, 17 Dec 2003 10:47:43 +0000
Subject: [PATCH] Merge from branch 19
---
modules/Bio/EnsEMBL/Lite/SNPAdaptor.pm | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/modules/Bio/EnsEMBL/Lite/SNPAdaptor.pm b/modules/Bio/EnsEMBL/Lite/SNPAdaptor.pm
index 168fb3cb45..ec68696b67 100644
--- a/modules/Bio/EnsEMBL/Lite/SNPAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Lite/SNPAdaptor.pm
@@ -84,6 +84,9 @@ sub fetch_all_by_Slice {
}
#create a snp object through a fast (hacky) constructor
+ my $STATUS = $arrayref->[6];
+ $STATUS =~s/-/ /;
+ $STATUS = $STATUS eq 'no info' ? 'suspected' : "proven $STATUS";
my $snp = Bio::EnsEMBL::SNP->new_fast(
{ 'dbID' => $arrayref->[0],
'_gsf_start' => $arrayref->[1] - $slice_start + 1,
@@ -93,10 +96,12 @@ sub fetch_all_by_Slice {
'_type' => $arrayref->[4],
'_range_type' => $arrayref->[5],
'_validated' => $arrayref->[6],
+ 'status' => $STATUS,
'alleles' => $arrayref->[7],
'_ambiguity_code' => $arrayref->[10],
'_snpclass' => $arrayref->[8],
'_mapweight' => $arrayref->[9],
+ '_source' => $arrayref->[11],
'_source_tag' => $arrayref->[11],
'link' => \@links });
push @snps, $snp;
--
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