Add note about Boost 1.48

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118278]
Clean up long lines

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118279]
Add a bite-sized Quiver test based on some hepatitus C virus data

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118280]
Nuke trailing whitespace

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118289]
Make test_rare.py non-executable so nose won't ignore it.

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118290]
Append "|plurality" to FASTA header for plurality consensus output.

Also some needed cleanup: `consumers` interface only used by plurality.

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118291]
For -w, look up reference name flexibly as either: header, name, or id

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118304]
Expunge almost all remaining vestiges of "ref000..." output from
logging outputs

The only place it remains is in the --dumpEvidence output, where it is
needed in order to create path names

[Tracking bug 21562]

Signed-off-by: David Alexander <dalexander@ucla.edu>

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118305]
Restore one of the whitespaces ... which actually was important for a test

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118336]
Remove ref to deleted files

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118399]
FASTQ header should agree with FASTA

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118400]
Make small-quiver-test a little more literate

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118401]
Add `lowercasereference` as a possible argument for --noEvidenceConsensusCall

When enabled, genomic windows with inadequate coverage to yield
accurate consensus are filled in the consensus output (FASTA, FASTQ)
with the lowercased reference bases.

Experimentally enable this mode to help identify test failures.

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118402]
Bump h5py requirement to >= 2.0.1

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118403]
Bump GenomicConsensus version to 0.5.0

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118404]
Fix a couple issues with `lowercasereference` change

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 118411]