Ensembl/ensembl-webcode — pull request #115 by muffato (2014-09-30 18:14:24+00:00)
Title: Only list self-alignments with haplotypes/patches

Since Compara now has in the same dataset human self-alignments for
chromosomes, unplaced contigs, and haplotypes, we cannot rely simply
on the method_link_type (previously != "ucsc").
Instead, we need to select the alignment blocks that contain a non-primary
region (is_reference=0)

The code should still work for VEGA as they use the method_link_type "LASTZ_RAW"

Examples:
no haplotypes -> nothing listed: http://enssand-01.internal.sanger.ac.uk:9073/Homo_sapiens/Location/Multi?db=core;g=ENSG00000167618;r=19:37211278-37268525
haplotypes -> listed: http://enssand-01.internal.sanger.ac.uk:9073/Homo_sapiens/Location/Multi?db=core;g=ENSG00000167618;r=6:31501024-32001023