Review classification of chromosome/scaffold

[jmmut]

We allow enabling or disabling scaffold ingestion at compile time, but the classification of a sequence as "chromosome" or "scaffold" may not be completely right:

            if (!line.startsWith("#")) {
                parseChromosomeLine(line);
                String[] columns = line.split("\t", -1);
                if (columns.length >= 6) {
                    if (columns[3].equals("Chromosome")) {
                        parseChromosomeLine(columns);
                    } else if (isScaffoldsEnabled && columns[1].equals("unplaced-scaffold")) {
                        parseScaffoldLine(columns);
                    }
                }

for instance, the MT (in ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.14_GRCh37.p13/) won't be considered as either chromosome nor scaffold because its column[3] is Mitochondrion, not Chromosome, and its column[1] is assembled-molecule, not unplaced-scaffold.

Likewise, there are other contigs that are different to unplaced-scaffold. GCA_000001405.14 has some of them, like alt-scaffold, fix-patch and others, and we should decide whether to include them and in which category if so. (Including as Chromosome is meant for a small set of very used sequences, scaffolds for anything else).