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JAL-2975,JAL-2647,JAL-1767,JAL-2965, JAL-3111 updated PCA viewer documentation
[jalview.git]
/
src
/
jalview
/
io
/
vcf
/
VCFLoader.java
diff --git
a/src/jalview/io/vcf/VCFLoader.java
b/src/jalview/io/vcf/VCFLoader.java
index
9831af7
..
7bf7791
100644
(file)
--- a/
src/jalview/io/vcf/VCFLoader.java
+++ b/
src/jalview/io/vcf/VCFLoader.java
@@
-100,10
+100,12
@@
public class VCFLoader
*/
private static final String VCF_ASSEMBLY = "VCF_ASSEMBLY";
*/
private static final String VCF_ASSEMBLY = "VCF_ASSEMBLY";
- private static final String DEFAULT_VCF_ASSEMBLY = "assembly19=GRCh38,hs37=GRCh37,grch37=GRCh37,grch38=GRCh38";
+ private static final String DEFAULT_VCF_ASSEMBLY = "assembly19=GRCh37,hs37=GRCh37,grch37=GRCh37,grch38=GRCh38";
private static final String VCF_SPECIES = "VCF_SPECIES"; // default is human
private static final String VCF_SPECIES = "VCF_SPECIES"; // default is human
+ private static final String DEFAULT_REFERENCE = "grch37"; // fallback default is human GRCh37
+
/*
* keys to fields of VEP CSQ consequence data
* see https://www.ensembl.org/info/docs/tools/vep/vep_formats.html
/*
* keys to fields of VEP CSQ consequence data
* see https://www.ensembl.org/info/docs/tools/vep/vep_formats.html
@@
-263,7
+265,12
@@
public class VCFLoader
public SequenceI loadVCFContig(String contig)
{
VCFHeaderLine headerLine = header.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
public SequenceI loadVCFContig(String contig)
{
VCFHeaderLine headerLine = header.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
- String ref = headerLine == null ? null : headerLine.getValue();
+ if (headerLine == null)
+ {
+ Cache.log.error("VCF reference header not found");
+ return null;
+ }
+ String ref = headerLine.getValue();
if (ref.startsWith("file://"))
{
ref = ref.substring(7);
if (ref.startsWith("file://"))
{
ref = ref.substring(7);
@@
-282,7
+289,7
@@
public class VCFLoader
}
else
{
}
else
{
- System.err.println("VCF reference not found: " + ref);
+ Cache.log.error("VCF reference not found: " + ref);
}
return seq;
}
return seq;
@@
-301,7
+308,7
@@
public class VCFLoader
{
VCFHeaderLine ref = header
.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
{
VCFHeaderLine ref = header
.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
- String reference = ref.getValue();
+ String reference = ref == null ? null : ref.getValue();
setSpeciesAndAssembly(reference);
setSpeciesAndAssembly(reference);
@@
-373,8
+380,13
@@
public class VCFLoader
*/
protected void setSpeciesAndAssembly(String reference)
{
*/
protected void setSpeciesAndAssembly(String reference)
{
+ if (reference == null)
+ {
+ Cache.log.error("No VCF ##reference found, defaulting to "
+ + DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES);
+ reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified
+ }
reference = reference.toLowerCase();
reference = reference.toLowerCase();
- vcfSpecies = DEFAULT_SPECIES;
/*
* for a non-human species, or other assembly identifier,
/*
* for a non-human species, or other assembly identifier,
@@
-397,6
+409,7
@@
public class VCFLoader
}
}
}
}
+ vcfSpecies = DEFAULT_SPECIES;
prop = Cache.getProperty(VCF_SPECIES);
if (prop != null)
{
prop = Cache.getProperty(VCF_SPECIES);
if (prop != null)
{
@@
-724,7
+737,7
@@
public class VCFLoader
String species = seqCoords.getSpeciesId();
String chromosome = seqCoords.getChromosomeId();
String seqRef = seqCoords.getAssemblyId();
String species = seqCoords.getSpeciesId();
String chromosome = seqCoords.getChromosomeId();
String seqRef = seqCoords.getAssemblyId();
- MapList map = seqCoords.getMap();
+ MapList map = seqCoords.getMapping();
// note this requires the configured species to match that
// returned with the Ensembl sequence; todo: support aliases?
// note this requires the configured species to match that
// returned with the Ensembl sequence; todo: support aliases?