bcbio.variation.variantcontext
Helper functions to retrieve information from htsjdk VariantContext objects, which represent variant data stored in VCF files.
Helper functions to retrieve information from htsjdk VariantContext objects, which represent variant data stored in VCF files.
create-ref-dictclj
(create-ref-dict ref-file)Create reference dictionaries required by GATK and Picard. Requires samtools command to create *.fai if missing, since code to create these is no longer present in GATK.
Create reference dictionaries required by GATK and Picard. Requires samtools command to create *.fai if missing, since code to create these is no longer present in GATK.
from-genotypeclj
(from-genotype g)Represent a sample genotype including alleles. :genotype stores the original java genotype object for direct access.
Represent a sample genotype including alleles. :genotype stores the original java genotype object for direct access.
from-vcclj
(from-vc vc)Provide a top level map of information from a variant context. :vc stores the original java VariantContext object for direct access.
Provide a top level map of information from a variant context. :vc stores the original java VariantContext object for direct access.
get-seq-dictclj
(get-seq-dict ref-file)Retrieve Picard sequence dictionary from FASTA reference file.
Retrieve Picard sequence dictionary from FASTA reference file.
get-vcf-headerclj
(get-vcf-header vcf-file)Retrieve header from input VCF file.
Retrieve header from input VCF file.
get-vcf-iteratorclj
(get-vcf-iterator in-file)(get-vcf-iterator in-file ref-file)Create an iterator over VCF VariantContexts.
Create an iterator over VCF VariantContexts.
get-vcf-retrieverclj
(get-vcf-retriever ref & vcf-files)Indexed variant file retrieval for zero to multiple files with clean handle closing.
Indexed variant file retrieval for zero to multiple files with clean handle closing.
get-vcf-samplesclj
(get-vcf-samples vcf-file)Retrieve samples from a VCF header
Retrieve samples from a VCF header
get-vcf-sourceclj
(get-vcf-source in-file)(get-vcf-source in-file ref-file)Create a Tribble FeatureSource for VCF file, using bgzipped tabix indexed VCFs.
Create a Tribble FeatureSource for VCF file, using bgzipped tabix indexed VCFs.
parse-vcfclj
(parse-vcf vcf-source)Lazy iterator of VariantContext information from VCF file.
Lazy iterator of VariantContext information from VCF file.
remove-filterclj
(remove-filter vc)Remove filter from a variant context.
Remove filter from a variant context.
variants-in-regionclj
(variants-in-region retriever vc)(variants-in-region retriever space start end)Retrieve variants located in potentially multiple variant files
Retrieve variants located in potentially multiple variant files
vc-add-attrclj
(vc-add-attr vc key val)Add an attribute to the current VariantContext
Add an attribute to the current VariantContext
write-vcf-w-templateclj
(write-vcf-w-template tmpl-file
out-file-map
vc-iter
&
{:keys [header-update-fn new-md]})Write VCF output files starting with an original input template VCF.
Handles writing to multiple VCF files simultaneously with the different
file handles represented as keywords. This allows lazy splitting of VCF files:
vc-iter is a lazy sequence of (writer-keyword variant-context).
out-file-map is a map of writer-keywords to output filenames.
Write VCF output files starting with an original input template VCF. Handles writing to multiple VCF files simultaneously with the different file handles represented as keywords. This allows lazy splitting of VCF files: `vc-iter` is a lazy sequence of `(writer-keyword variant-context)`. `out-file-map` is a map of writer-keywords to output filenames.
cljdoc is a website building & hosting documentation for Clojure/Script libraries
× close