Package org.snpsift.annotate

Class AnnotateVcfDb

    • Constructor Summary

      Constructors 
      Constructor Description
      AnnotateVcfDb()  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean annotate​(org.snpeff.vcf.VcfEntry vcfEntry)
      Annotate a VCF entry
      protected boolean annotateExists​(org.snpeff.vcf.VcfEntry vcfEntry)
      Add 'exists' flag to INFO fields
      protected boolean annotateIds​(org.snpeff.vcf.VcfEntry vcfEntry, java.util.Set<java.lang.String> idSet)
      Add ID information.
      protected boolean annotateInfo​(org.snpeff.vcf.VcfEntry vcfEntry, java.util.Map<java.lang.String,​java.lang.String> info)
      Add INFO fields.
      void close()  
      protected void discoverInfoFields()  
      protected void discoverInfoFields​(org.snpeff.vcf.VcfEntry dbVcfEntry)
      If 'ALL' info fields are being used, we can try to discover new fields that have not already been added to the annotation list (e.g.
      java.util.List<org.snpeff.vcf.VcfEntry> find​(org.snpeff.interval.Variant var)  
      java.util.List<org.snpeff.vcf.VcfEntry> find​(org.snpeff.vcf.VcfEntry vcfEntry)
      Find matching entries in the database
      protected boolean findDbExists​(QueryResult qr)
      Should we annotate using 'exists' field?
      protected void findDbId​(java.util.Set<java.lang.String> idSet, QueryResult qr)
      Find an ID for this variant and add them to idSet
      protected java.lang.String findDbInfo​(java.lang.String infoFieldName, QueryResult qr)
      Find all non-empty INFO fields 'infoFieldName' in results
      protected void findDbInfo​(java.util.Map<java.lang.String,​java.lang.String> info, QueryResult qr)
      Find INFO fields for this VCF entry
      protected java.lang.String findDbInfoAlt​(java.lang.String infoFieldName, QueryResult qr)
      Find the first non-empty INFO field 'infoFieldName' in results Note: ALT must match
      protected void findDbInfoRef​(java.util.Map<java.lang.String,​java.lang.String> info, java.util.Set<org.snpeff.vcf.VcfEntry> uniqueVcfEntries)
      Fill values for INFO fields requiring 'REF' value
      protected boolean match​(org.snpeff.interval.Variant var, org.snpeff.vcf.VariantVcfEntry dbEntry)
      Does database entry 'dbVcfEntry' match 'variant'?
      void open()  
      protected java.lang.String prependInfoName​(java.lang.String infoStr)
      Prepend 'prependInfoFieldName' to all info fields
      protected java.util.Collection<org.snpeff.vcf.VariantVcfEntry> query​(org.snpeff.interval.Variant variant)
      Query database and find results matching 'variant'
      void setAnnotateEmpty​(boolean annotateEmpty)  
      void setDebug​(boolean debug)  
      void setExistsInfoField​(java.lang.String existsInfoField)  
      void setInfoFields​(boolean useInfoFields, java.util.Collection<java.lang.String> infoFields)  
      void setPrependInfoFieldName​(java.lang.String prependInfoFieldName)  
      void setUseId​(boolean useId)  
      void setUseRefAlt​(boolean useRefAlt)  
      void setVerbose​(boolean verbose)  
      java.lang.String toString()  
      protected java.lang.String uniqueIds​(java.util.Set<java.lang.String> idSetDb, java.lang.String idStrVcf)
      IDs from database not present in VCF
      protected void warn​(java.lang.String warn)
      Show a warning message (up to MAX_ERRORS times)

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

    • Field Detail

      • verbose

        protected boolean verbose

      • debug

        protected boolean debug

      • annotateEmpty

        protected boolean annotateEmpty

      • hasVcfInfoPerAlleleRef

        protected boolean hasVcfInfoPerAlleleRef

      • useId

        protected boolean useId

      • useInfoFields

        protected boolean useInfoFields

      • useAllInfoFields

        protected boolean useAllInfoFields

      • useRefAlt

        protected boolean useRefAlt

      • chrPrev

        protected java.lang.String chrPrev

      • existsInfoField

        protected java.lang.String existsInfoField

      • prependInfoFieldName

        protected java.lang.String prependInfoFieldName

      • dbVcf

        protected DbVcf dbVcf

      • vcfDbFile

        protected org.snpeff.fileIterator.VcfFileIterator vcfDbFile

      • errCount

        protected java.util.HashMap<java.lang.String,​java.lang.Integer> errCount

      • infoFields

        protected java.util.Set<java.lang.String> infoFields

      • vcfInfoPerAllele

        protected java.util.Map<java.lang.String,​java.lang.Boolean> vcfInfoPerAllele

      • vcfInfoPerAlleleRef

        protected java.util.Map<java.lang.String,​java.lang.Boolean> vcfInfoPerAlleleRef

    • Constructor Detail

      • AnnotateVcfDb

        public AnnotateVcfDb()

    • Method Detail

      • annotate

        public boolean annotate​(org.snpeff.vcf.VcfEntry vcfEntry)
                 throws java.io.IOException
        Annotate a VCF entry
        Throws:
        java.io.IOException

      • annotateExists

        protected boolean annotateExists​(org.snpeff.vcf.VcfEntry vcfEntry)
        Add 'exists' flag to INFO fields

      • annotateIds

        protected boolean annotateIds​(org.snpeff.vcf.VcfEntry vcfEntry,
                              java.util.Set<java.lang.String> idSet)
        Add ID information. Make sure we are no repeating IDs

      • annotateInfo

        protected boolean annotateInfo​(org.snpeff.vcf.VcfEntry vcfEntry,
                               java.util.Map<java.lang.String,​java.lang.String> info)
        Add INFO fields.

      • close

        public void close()

      • discoverInfoFields

        protected void discoverInfoFields()

      • discoverInfoFields

        protected void discoverInfoFields​(org.snpeff.vcf.VcfEntry dbVcfEntry)
        If 'ALL' info fields are being used, we can try to discover new fields that have not already been added to the annotation list (e.g. implicit fields not mentioned in the VCF header)

      • find

        public java.util.List<org.snpeff.vcf.VcfEntry> find​(org.snpeff.interval.Variant var)

      • find

        public java.util.List<org.snpeff.vcf.VcfEntry> find​(org.snpeff.vcf.VcfEntry vcfEntry)
        Find matching entries in the database

      • findDbExists

        protected boolean findDbExists​(QueryResult qr)
        Should we annotate using 'exists' field?

      • findDbId

        protected void findDbId​(java.util.Set<java.lang.String> idSet,
                        QueryResult qr)
        Find an ID for this variant and add them to idSet

      • findDbInfo

        protected void findDbInfo​(java.util.Map<java.lang.String,​java.lang.String> info,
                          QueryResult qr)
        Find INFO fields for this VCF entry

      • findDbInfo

        protected java.lang.String findDbInfo​(java.lang.String infoFieldName,
                                      QueryResult qr)
        Find all non-empty INFO fields 'infoFieldName' in results

      • findDbInfoAlt

        protected java.lang.String findDbInfoAlt​(java.lang.String infoFieldName,
                                         QueryResult qr)
        Find the first non-empty INFO field 'infoFieldName' in results Note: ALT must match

      • findDbInfoRef

        protected void findDbInfoRef​(java.util.Map<java.lang.String,​java.lang.String> info,
                             java.util.Set<org.snpeff.vcf.VcfEntry> uniqueVcfEntries)
        Fill values for INFO fields requiring 'REF' value

      • match

        protected boolean match​(org.snpeff.interval.Variant var,
                        org.snpeff.vcf.VariantVcfEntry dbEntry)
        Does database entry 'dbVcfEntry' match 'variant'?

      • open

        public void open()

      • prependInfoName

        protected java.lang.String prependInfoName​(java.lang.String infoStr)
        Prepend 'prependInfoFieldName' to all info fields

      • query

        protected java.util.Collection<org.snpeff.vcf.VariantVcfEntry> query​(org.snpeff.interval.Variant variant)
        Query database and find results matching 'variant'

      • setAnnotateEmpty

        public void setAnnotateEmpty​(boolean annotateEmpty)

      • setDebug

        public void setDebug​(boolean debug)

      • setExistsInfoField

        public void setExistsInfoField​(java.lang.String existsInfoField)

      • setInfoFields

        public void setInfoFields​(boolean useInfoFields,
                          java.util.Collection<java.lang.String> infoFields)

      • setPrependInfoFieldName

        public void setPrependInfoFieldName​(java.lang.String prependInfoFieldName)

      • setUseId

        public void setUseId​(boolean useId)

      • setUseRefAlt

        public void setUseRefAlt​(boolean useRefAlt)

      • setVerbose

        public void setVerbose​(boolean verbose)

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • uniqueIds

        protected java.lang.String uniqueIds​(java.util.Set<java.lang.String> idSetDb,
                                     java.lang.String idStrVcf)
        IDs from database not present in VCF

      • warn

        protected void warn​(java.lang.String warn)
        Show a warning message (up to MAX_ERRORS times)