The VCF format (
http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
)
specifies "." to represent missing values.
lib/galaxy/visualization/tracks/data_providers.py throws an float conversion error when
the qual field of a vcf file has the missing value: "."
This can be remedied with the following patch, trackster handles the "None"
value when displaying the variant.
diff -r eb542e228a0f lib/galaxy/visualization/tracks/data_providers.py
--- a/lib/galaxy/visualization/tracks/data_providers.py Wed Aug 22 14:56:49
2012 -0500
+++ b/lib/galaxy/visualization/tracks/data_providers.py Wed Aug 22 14:58:46
2012 -0500
@@ -634,7 +634,7 @@
# TODO? VCF does not have strand, so default to
positive.
"+",
new_seq,
- float( feature[5] ) ]
+ None if feature[5] == '.' else float( feature[5] )
]
rval.append(payload)
return { 'data': rval, 'message': message }
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