Improved sequence id extraction from filenames and sequence headers.
The default setting works a bit smarter now, it first tries to find NCBI-style accession or accession.version identifiers, then genbank identifiers and finally uses the filename (without path and extension).
The new command line option -sequence-id-format <type> allows the user to select a preferred method for sequence id extraction.
Available values for <type> are:
smart: (default), works as described abovencbi: only use NCBI-style accession or accession.version identifiersgenbank: only use genbank identifiersfilename: only use filename (without path and extension)leadingword: only use first contiguous stretch of non-whitespace characters