Multiple alleles for each strain are now added to the sqlDB, something
in BlastResults.pm is not right.
Commit before switch
Fixed the check in PanGenome.pm
PanGenome runs without incident, however the results in pan_genome.txt
look like they are taking the _-a3 version in preference to the first.
Pointing all strain variations at the same contig table -- this however
does not allow multiple values. Need to change.
Start of returning results as an array, not a hash, to allow multiple
results per genome name (for multiple alleles)
sub now returns the genome names that have results for the given query
sequence.
first pass, _processBlastXML cleaned up to use array of results
_getMsa updated to use the array of results. It is actually simpler than
the previous hash way.
First pass, _getCoreResult is modified.
Storing allele information.
Modified _getHashOfFastaAlignment to be only one level deep.
Fixed sequence due to refactored _getHashOfMSA in PanGenome.pm
Saving for later.
Changed to overwrite the output if exists, will revert after branch is
done
Added the 'overwrite' flag, which will delete the output directory if it
exists. If this is not set, or set to 0, it exits and tells the user the
directory already exists.
Fixed the allele count bug, where the entire hash was not being reset,
only the last key that was found.
Fixed bug where the MSA used the header, the hash used
SequenceName->name, and the DB insert used the header. Now all use the
header, will need to workout how to deal with multiple copies per
genome.
Getting the genome names to determine core / accessory now uses the
SequenceName module; thus, 3 alleles from one genome only counts for 1,
not 3.
Modified the SNP finder to use the array style of result, as well as
multiple alleles.