Update test code for the new `lowercasereference` default.

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118417]
       Update test file to match change to reference name (removed ref000001 string)

       [Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118461]
       Add quiver integration test for one of the Eichler BACs.

       [Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118464]
Ensure variants are sorted before writing to file

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118491]
Update documentation

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118505]