searchHashTable: Search hash table

In janmatula/genDP: Tools for genotyping data processing

Description

Searches hash table obtained using the buildHashTable function for occurences of query sequences from FASTA file.

Usage

searchHashTable(querySequences, hashTable, k = 10, results = 1,
  tolerance = 1)

Arguments

querySequences	FASTA file containing sequences we are searching for
hashTable	output of buildHashTable function
k	number of bases the query sequences are divided into, must be the same as in buildHashTable
results	number of top results of the SSAHA method that will be provie in the outpus list
tolerance	tolerance for insertions and deletions in number of nucleotides

Value

A list of matrices containg best matches and score for each query sequence.

Examples

searchHashTable("query.fasta", hashTable, k=10, results = 10, tolerance = 5)

janmatula/genDP documentation built on Feb. 2, 2021, 7 p.m.