- <init>
Open the given indexed fasta sequence file. Throw an exception if the file
cannot be opened.
- getSubsequenceAt
Gets the subsequence of the contig in the range [start,stop]
- canCreateIndexedFastaReader
- getSequenceDictionary
Retrieves the sequence dictionary for the fasta file.
- findFastaIndex
- findRequiredFastaIndexFile
- close
- getSequence
Retrieves the complete sequence described by this contig.
- nextSequence
Gets the next sequence if available, or null if not present.
- reset
Reset the iterator over the index.
- sanityCheckDictionaryAgainstIndex
Do some basic checking to make sure the dictionary and the index match.