Merge pull request #1323 from melissalinkert/bit-ops

Add bit-level operations to RandomAccess{Input, Output}Stream
PCORAW: fix offsets for files larger than 4 GB
cmake: Add missing include directories

For platforms which do not have the headers on the standard
search path.
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1154 (Leica: prevent exception when linking EmissionFilter)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1302 (Add branch-specific link for downloading the JAR file if unfound (rebased onto develop))
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1328 (Use in-place caching by default in Memoizer)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1339 (Amaris FlowSight)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1343 (C++: TIFF pixel data read/write interfaces and skeleton implementation)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1347 (AIM: fix offset calculation for > 4GB files)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1348 (PCORAW: fix offsets for files larger than 4 GB)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1349 (cmake: Add missing include directories)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1309 melissalinkert 'Allow tile-based access of large JPEG-2000 images' (exclude comment)
  # PR 1265 qidane 'New units' (label: exclude breaking)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (label: exclude)
  # PR 1296 melissalinkert 'Add test for getRequiredDirectories' (label: exclude)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (label: exclude)
  # PR 1054 qidane 'Additional annotation points throughout the model' (exclude comment)
  # PR 1315 LeeKamentsky 'IM3Reader for Perkin-Elmer Nuance' (user: LeeKamentsky)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (label: exclude)
  # PR 1249 PremyslFiala 'ND2 - Bug fixes' (user: PremyslFiala)
Updating 32c7be8..46f4115
Previously merged:
  # PR 1323 melissalinkert 'Add bit-level operations to RandomAccess{Input, Output}Stream'

Merged PRs:
  # PR 1154 melissalinkert 'Leica: prevent exception when linking EmissionFilter'
  # PR 1302 sbesson 'Add branch-specific link for downloading the JAR file if unfound (rebased onto develop)'
  # PR 1328 sbesson 'Use in-place caching by default in Memoizer'
  # PR 1339 melissalinkert 'Amaris FlowSight'
  # PR 1343 rleigh-dundee 'C++: TIFF pixel data read/write interfaces and skeleton implementation'
  # PR 1347 melissalinkert 'AIM: fix offset calculation for > 4GB files'
  # PR 1348 melissalinkert 'PCORAW: fix offsets for files larger than 4 GB'
  # PR 1349 rleigh-dundee 'cmake: Add missing include directories'

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Update auto-generated documentation

Repository: snoopycrimecop/bioformats

Generated by BIOFORMATS-5.1-merge-docs-autogen#49 (http://ci.openmicroscopy.org/job/BIOFORMATS-5.1-merge-docs-autogen/49/)