Returns the next chunk of input sequences. Input sequences are split at non-ACGT characters and parts between those are returned independently.
For longer sequences that are split in this manner, the offsets of the individual chunks within the complete sequence are also returned.
read - the source of the sequence data
lastHeader - the header of previous chunk, may be empty initially and is modified internally
minimumLength - the minimum length of sequences or chunks considered, shorter sequences are skipped
a Pair with the offsets of the individual chunks and the sequences
IOException - if the sequence could not be read from read