Class VariantTypeCounter
java.lang.Object
org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
- All Implemented Interfaces:
Serializable
Count different types of variants
These statistics are used to create data sets
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Field Summary
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
count
(org.snpeff.vcf.VcfEntry vcfEntry) Count the number of variants in a VCF filestatic VariantTypeCounter
countVariants
(String vcfLines) Count variants in a string of VCF lines (i.e.int
getCount
(VariantCategory variantCategory) int[]
int
getSize
(VariantCategory variantCategory, String field) Get total size (in bytes) of a field (only string fields)toString()
protected void
updateSizes
(VariantCategory variantCategory, String field, String value) Update sizes for a field
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Field Details
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REF
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ALT
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fields
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fieldsString
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countByCategory
protected int[] countByCategory -
countVcfEntries
protected long countVcfEntries -
countVariants
protected long countVariants -
sizesByField
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Constructor Details
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VariantTypeCounter
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Method Details
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countVariants
Count variants in a string of VCF lines (i.e. a VCF file contents in a string) This is used for testing -
count
public void count(org.snpeff.vcf.VcfEntry vcfEntry) Count the number of variants in a VCF file -
getCount
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getCountByCategory
public int[] getCountByCategory() -
getFields
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getSize
Get total size (in bytes) of a field (only string fields)- Returns:
- Total size (in bytes) or -1 if the field is not found
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getSizesByField
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toString
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updateSizes
Update sizes for a field
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