New upstream version 4.0.0

BasedOnStyle:  Google

BreakBeforeBraces: Mozilla

AllowShortLoopsOnASingleLine: false

AccessModifierOffset: -4

BreakConstructorInitializersBeforeComma: true

ColumnLimit: 100

IndentWidth: 4

PointerAlignment: Left

TabWidth: 4

ReflowComments: false  # protect ASCII art in comments

KeepEmptyLinesAtTheStartOfBlocks: true

tests/data/julietflow/flea99_97_1.bam filter=lfs diff=lfs merge=lfs -text

tests/data/julietflow/hxb2.fasta filter=lfs diff=lfs merge=lfs -text

.DS_Store

/build

/_deps

/_rev_deps

/unyve

# Meson WrapDB stuff

subprojects/packagecache/

subprojects/googletest*

subprojects/pbbam*

subprojects/pbcopper*

[submodule "third-party/pbbam"]

    path = third-party/pbbam

    url = ../pbbam.git

    branch = develop

[submodule "third-party/seqan"]

    path = third-party/seqan

    url = ../seqan.git

    branch = develop

[submodule "third-party/pbcopper"]

    path = third-party/pbcopper

    url = ../pbcopper.git

    branch = develop

# UNANIMITY - CHANGELOG

## [3.1.0]

### Changed

 - Per ZMW timings are default on in DIAGNOSTICS mode or available via hidden

   option --zmwTimings. Output is BAM tag ms

## [3.0.0]

### Refactored

 - MultiMolecularIntegrator renamed to just Integrator

 - MonoMolecularIntegrator removed, all integrators now accept multiple molecules

 - VirtualTemplate removed, as without MonoMolecular it is no longer needed

 - MutatedTemplate added as a View object over some const template

 - Template::Mutate() now returns a MutatedTemplate instead of modifying the Template

 - Template was promoted from a member of Recursor to a member of EvaluatorImpl

 - Recursor refactored to take a template as an argument in most functions

 - Existing model files updated to match the new parent Recursor class

 - s/PB_CHEMISTRY_BUNDLE_DIR/SMRT_CHEMISTRY_BUNDLE_DIR/g

## [2.1.0]

### Added

 - Use pbcopper's q-gram index for sparse alignment

 - Replaced seqan MSA in ChimeraLabeler

 - support loading bundle models from PB_CHEMISTRY_BUNDLE_DIR

   environment variable

## [2.0.4]

### Added

 - Add pbcopper's ToolContract, summary is no longer a second output file

 - Differentiate between .xml and .bam output type

 - Enforce .pbi generation

## [2.0.3]

### Added

 - Switch from cpp-optparse to pbcopper, use pbcopper's CLI parsing

## [2.0.2]

### Added

 - Fix index errors in the Hirschberg aligner

 - Added a cleaner interface for AddRead/GetTemplate

## [2.0.1]

### Added

 - Add new ReleaseWithAssert CMAKE_BUILD_TYPE

 - Bump version (to cc2 + ccs)

 - Unify CCS and CC2 versioning under unanimity

 - Cleanup python/swig generation

 - Cleanup version handling

## [0.0.1]

### Added

 - Unify code base, refactor directory structure

 - Add pbccs, ConsensusCore2, pbsparse, and pbchimera

 - Code coverage report

 - Initial framework including pbbam, htslib, pbcopper