Constructor Detail

Method Detail

• createAlleleList

   static List<String> createAlleleList(VariantContext vc)

  createALleleList returns an array list containing just the ref allele string, if the VariantContext record is a ref record. Or both the ref allele and first alt allele, if the VariantContext record is a variant record. THis method does not check if the allele exists. The returned list is ALL alleles - this assumes they will be added via an INSERT/IGNORE db command.

• createAlleleList

   static List<String> createAlleleList(HaplotypeNode.VariantInfo vi)

  Method to create a list of alleles based on if the variant info is a ref or variant.

• getVariantData

   static Tuple<String, VariantMappingData> getVariantData(String chrom, Map<String, Integer> alleleHashMap, HaplotypeNode.VariantInfo vi, Connection dbConn)

  Method will return a Tuple of the hash of (chrom, start_position, refAlleleID, altAlleleID) and a VariantMappingData record The alleleHashMap should contain the initial alleles pre-populated. If the alleleId cannot be found from this hash map, the db will be queried. Generally 2/3 of all alleles will be found on the hashmap.

• getLongListOfVariantData

   static List<Long> getLongListOfVariantData(List<Tuple<String, VariantMappingData>> variantMappingDataList, Map<String, Integer> hashIDMap)

  Takes a list of variantIdhash to VariantMappingData and creates a list of "long" values, that represents the variant context for each entry

  Parameters:

  hashIDMap - Map of variant_hash to variantID

• getLongFromVMData

   static long getLongFromVMData(int vmID, VariantMappingData vmd)

  Takes an ID and a VariantMappingData object and creates a list of variant_ids with additional data.

• getLongRefRecord

   static long getLongRefRecord(int refLen, int refDepth, int startPos)

  Takes a reference length, depth and start position on the chromosome. Returns an encode long holding this information. format: 1bit=ref | 2 bytes 7 bits = refLength | 1 bytes=refDepth | 4 bytes=position on chrom

• getLongVariantRecord

   static long getLongVariantRecord(int vmID, int refDepth, int altDepth, byte isIndel, int otherData)

  Takes a variantMapping id, reference depth, alternate depth, indication as to if is an indel, and a dummy int Returns a long formatted with this data. format: 4 bytes= variant_mapping table id | 1 byte=refDepth | 1 byte=altDepth | 1 bytes=isIndel | 1 byte unused

• encodeVariantLongListToByteArray

   static Array<byte> encodeVariantLongListToByteArray(List<Long> variantLongList)

  Method takes a List of Long objects and converts to a Snappy compressed byte stream

• decodeByteArrayToVariantLongList

   static List<Long> decodeByteArrayToVariantLongList(Array<byte> encodedByteArray)

  Method takes a Snappy compressed byte stream and decodes it into a List of Long objects

• longListToByteArray

   static Array<byte> longListToByteArray(Collection<Long> ListOfLongs)

  Parameters:

  ListOfLongs - a List or Collection of Longs to be converted into a byte[] array

• byteArrayToLongList

   static List<Long> byteArrayToLongList(Array<byte> byteArray)

  Parameters:

  byteArray - an array of bytes converting longs

• findAlleleIDFromDB

   static int findAlleleIDFromDB(String allele, Connection dbConn)

  From an allele string, compute the hash value and search for a corresponding ID in the DB alleles table.