Reapply BAM changes

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 141602]
Get the `bam2` branch working with the current BAM spec

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 141603]
Fix tests

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 141604]
Implicitly disable fancyChunking for BAM

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 141605]
Fix parsing of DS with trailing ';'

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 141649]
Quiver/BAM: Handle contig names uniformly, *always* using the "id" part of the header as the identifier

Per discussion with Marcus, we also will need to update the reference
uploader to bring it in line with its spec, where it claims it will
reject FASTAs with contigs with "id" values that are not unique.

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 142108]
Mark release 0.9.1; requires pbcore 0.9.1

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 142133]
   Bug 25700. Pass along the return code from ToolRunner.main.

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 142138]
   Bug 25931. Fix memory leak in BamReader.fetch by setting reopen to False.	

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 142242]
BAM/Quiver: Fix readLength

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 142372]
BAM/Quiver: Fix copy-and-paste error

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 142524]
BAM/Quiver: Remove cruft; implement position accessors

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 142525]
BAM/Quiver: Decorators for gating on having reference, index

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 142526]
BAM/Quiver: Tests

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 142527]
BAM/Quiver: fix test, check that `orientation` has a correct value.

Also factor gapify more cleanly.

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 142528]
BAM/Quiver: Get reference() working

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 142529]
BAM/Quiver: Get clipping working again

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 142530]
BAM/Quiver: Get "transcript" working

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 142531]
BAM/Quiver: printing works

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 142532]
BAM/Quiver: need to reset before iteration

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/tools/GenomicConsensus/": change = 142533]