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biospectra's Issues

Optimistic query term drop for kgrams

Drop redundant terms in case described below:
Query: AAAABBBBCCCC (4mers)
to AAAA, AABB, BBBB, BBCC, CCCC
drop AAAB, ABBB, BCCC
when AAAA, AABB, BBBB, BBCC, CCCC returns the same results (meaning no search for dropping kgrams are redundant)

Replace FASTA parser

Current FASTA parser uses String class as a data structure of parsed read.

  • parse "GI" in header
  • handle very long sequence in a read (up to GB scale) using InputStream.

Fasta File as a query

Take Fasta file as a query file. So that metagenomic sample file will be taken as an input of search system.

This will output:

  • matching reads : total count, organism, confidence score
  • unknown reads : total count

Document scoring

Need to research what scoring function default lucene uses.
Need to optimize it for better performance and confidence.

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