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JAL-2835 take all CSQ fields; catch invalid field match patterns
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 15 Nov 2017 10:50:19 +0000
(10:50 +0000)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 15 Nov 2017 10:50:19 +0000
(10:50 +0000)
src/jalview/io/vcf/VCFLoader.java
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diff --git
a/src/jalview/io/vcf/VCFLoader.java
b/src/jalview/io/vcf/VCFLoader.java
index
960615a
..
2847bd7
100644
(file)
--- a/
src/jalview/io/vcf/VCFLoader.java
+++ b/
src/jalview/io/vcf/VCFLoader.java
@@
-1,14
+1,5
@@
package jalview.io.vcf;
package jalview.io.vcf;
-import htsjdk.samtools.util.CloseableIterator;
-import htsjdk.variant.variantcontext.Allele;
-import htsjdk.variant.variantcontext.VariantContext;
-import htsjdk.variant.vcf.VCFHeader;
-import htsjdk.variant.vcf.VCFHeaderLine;
-import htsjdk.variant.vcf.VCFHeaderLineCount;
-import htsjdk.variant.vcf.VCFHeaderLineType;
-import htsjdk.variant.vcf.VCFInfoHeaderLine;
-
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Dna;
import jalview.api.AlignViewControllerGuiI;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Dna;
import jalview.api.AlignViewControllerGuiI;
@@
-37,6
+28,16
@@
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.regex.Pattern;
import java.util.Map;
import java.util.Map.Entry;
import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
+
+import htsjdk.samtools.util.CloseableIterator;
+import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.VariantContext;
+import htsjdk.variant.vcf.VCFHeader;
+import htsjdk.variant.vcf.VCFHeaderLine;
+import htsjdk.variant.vcf.VCFHeaderLineCount;
+import htsjdk.variant.vcf.VCFHeaderLineType;
+import htsjdk.variant.vcf.VCFInfoHeaderLine;
/**
* A class to read VCF data (using the htsjdk) and add variants as sequence
/**
* A class to read VCF data (using the htsjdk) and add variants as sequence
@@
-56,7
+57,7
@@
public class VCFLoader
private static final String DEFAULT_VCF_FIELDS = "AF,AC*";
private static final String DEFAULT_VCF_FIELDS = "AF,AC*";
- private static final String DEFAULT_VEP_FIELDS = "Allele,Consequence,IMPACT,SWISSPROT,SIFT,PolyPhen,CLIN_SIG";
+ private static final String DEFAULT_VEP_FIELDS = ".*";// "Allele,Consequence,IMPACT,SWISSPROT,SIFT,PolyPhen,CLIN_SIG";
/*
* keys to fields of VEP CSQ consequence data
/*
* keys to fields of VEP CSQ consequence data
@@
-156,7
+157,7
@@
public class VCFLoader
al = alignment;
// map of species!chromosome!fromAssembly!toAssembly to {fromRange, toRange}
al = alignment;
// map of species!chromosome!fromAssembly!toAssembly to {fromRange, toRange}
- assemblyMappings = new HashMap<String, Map<int[], int[]>>();
+ assemblyMappings = new HashMap<>();
}
/**
}
/**
@@
-420,7
+421,13
@@
public class VCFLoader
String[] tokens = pref.split(",");
for (String token : tokens)
{
String[] tokens = pref.split(",");
for (String token : tokens)
{
+ try
+ {
patterns.add(Pattern.compile(token.toUpperCase()));
patterns.add(Pattern.compile(token.toUpperCase()));
+ } catch (PatternSyntaxException e)
+ {
+ System.err.println("Invalid pattern ignored: " + token);
+ }
}
return patterns;
}
}
return patterns;
}