String desc = id.substring(space + 1);
seq.setDescription(desc);
- if (desc.startsWith("chromosome"))
- {
- /*
- * parse Ensembl style gene description e.g.
- * chromosome:GRCh38:7:140696688:140721955:1
- */
- String[] tokens = desc.split(":");
- if (tokens.length > 3)
- {
- try
- {
- seq.setStart(Integer.parseInt(tokens[3]));
- } catch (NumberFormatException e)
- {
- // ignore
- }
- }
- }
+ /*
+ * it is tempting to parse Ensembl style gene description e.g.
+ * chromosome:GRCh38:7:140696688:140721955:1 and set the
+ * start position of the sequence, but this causes much confusion
+ * for reverse strand feature locations
+ */
}
else
{