Updated DB schema. 'results' table now takes both snp and binary data
with a 'type' field.
Updated the unlinking of _filtered.delta and _query_dbtemp.index files
Added locus table to _createOutput file for proper JOIN
Added WHERE clause to limit for snp/binary
_emptySqlBuffers now iterates through all tables in _sqlString
Allele file is now printed when the input is a queryFile rather than a
pan-genome created from input genomes. This means the allele data is not
stored for a pan-genome creation.
The database schema has also been modified to be more space efficient.
SNP and Binary tables and phylip files created correctly from the new
database schema.
Modified error on unsuccessful DB query.
Bug from last commit where only loci above coreGenomeThreshold were
being considered as part of the pan-genome fixed.
Updated the allele output, so that the current row is added to the
output buffer before printing.
Finalized the locus_alleles.fastas output from queryFile runs.
Added test data and a test suite to ensure non-breaking changes.
Updated README.md to include information on running the tests.
Updated test number to 13
Updated the README.md to include lib/panseq.pl path rather than simply
panseq.pl. Removed a debug print from output.t.
unlinking of blast output file
Alleles are now MSA before storing in the SQL database.
Thus, when output, they are already aligned.
Updated test suite to check for the MSA allele output.
Streamlined the output.t file.
output.t now uses a single core, to ensure identical file outputs.
Multiple cores change the id of the loci, although the data is the same.