Interchangably use IndexedFastaSequenceFile and BlockCompressedIndexedFastaSequenceFile

[dariober]

I need to create a FastaSequenceFile either from an indexed fasta file or from a block compressed and indexed fasta file. I'd like to use the resulting object without worrying whether it was created from one input or the other. For example, I'd like to do something like:

AbstractIndexedFastaSequenceFile faSeqFile = null
if (foo) {
    faSeqFile = new BlockCompressedIndexedFastaSequenceFile(myInput);
} else {
    faSeqFile = new IndexedFastaSequenceFile(SomeOtherInput);
}
// Now use faSeqFile regardless of where it came from

Is this possible? Thanks!

[lbergelson]

Yes! Take a look at ReferenceSequenceFileFactory.getReferenceSequenceFile() and friends. It returns a ReferenceSequenceFile which abstracts away the differences between the different fasta inputs.