Commit cec71ff4 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.0.6+dfsg

parent 7de6f9cd

.gitignore

+4 −82
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# This file is used to ignore files which are generated

# ----------------------------------------------------------------------------



*~

*.autosave

*.a

*.core

*.moc

*.o

*.obj

*.orig

*.rej

*.so

*.so.*

*_pch.h.cpp

*_resource.rc

*.qm

.#*

*.*#

core

!core/

tags

.DS_Store

.directory

*.debug

Makefile*

*.prl

*.app

moc_*.cpp

ui_*.h

qrc_*.cpp

Thumbs.db

*.res

*.rc

/.qmake.cache

/.qmake.stash



# qtcreator generated files

*.pro.user*

CMakeLists.txt.user



# xemacs temporary files

*.flc



# Vim temporary files

.*.swp



# Visual Studio generated files

*.ib_pdb_index

*.idb

*.ilk

*.pdb

*.sln

*.suo

*.vcproj

*vcproj.*.*.user

*.ncb

*.sdf

*.opensdf

*.vcxproj

*vcxproj.*

/build*



.vscode



# MinGW generated files

*.Debug

*.Release



# Python byte code

# cram

*.pyc



# Binaries

# --------

*.dll

*.exe



# Generated directories

bin

build

lib



# Meson WrapDB stuff

subprojects/packagecache/

subprojects/googletest*



# generated Doxyfile

*Doxyfile
 
/subprojects/*

!/subprojects/*.wrap

CHANGELOG.md

+77 −5
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@@ -3,13 +3,85 @@ 
All notable changes to this project will be documented in this file.

This project adheres to [Semantic Versioning](http://semver.org/).



**NOTE:** The current series (0.y.z) is under initial development. Anything may

change at any time. The public API should not be considered stable yet. Once we

lock down a version 1.0.0, this will define a reference point & compatibility

guarantees will be maintained within each major version series.



## Active



### Added

 - CCSRecord API to work with the minimally required data for CCS

 - TextFileReader & TextFileWriter for generic line files (plain text or gzipped)

 - BedReader & BedWriter for BED format support



## [1.0.6] - 2019-06-14



### Added

 - IFastaWriter & IFastqWriter abstract base classes



## [1.0.5] - 2019-06-11



### Changed

 - BAM tag lookup improvements under the hood.



## [1.0.4] - 2019-06-07



### Added

 - General-purpose BgzipWriter

 - BgzipFastaWriter and BgzipFastqWriter

 - Read-only view to read indices passing a PbiFilter

 - IPD field to SimpleRead



## [1.0.3] - 2019-05-20



### Added

 - IndexedFastqReader for random access to FASTQ subregions



### Fixed

 - MappedSimpleRead clipping: on disjoint aligned/requested regions and on requests larger

   than available sequence.



## [1.0.2] - 2019-05-10



### Added

 - Range-for iteration on FastaReader & FastqReader



## [1.0.1] - 2019-05-09



### Added

 - SimpleRead & MappedSimpleRead for htslib-free processing.



### Fixed

 - Incorrect type displayed in SAM output (pure-text) for floating-point values.



## [1.0.0] - 2019-04-22



### Changed

 - C++14 is now a *hard* minimum.



### Removed

 - Headers emulating C++14 features for C++11.



### Fixed

 - Inconsistent whitelist/blacklist filters in DataSet XML.



## [0.25.0] - 2019-04-11



### Changed

 - Requires C++14 at minimum.



### Fixed

 - Reading BioSample(s) elements from DataSet XML.



## [0.24.0] - 2019-04-05



### Added

 - Built-in support for dataset elements: BioSample(s) & DNABarcode(s).

 - BaiIndexCache for reusing data from *.bai files(s).

 - Support in GenomicIntervalQuery for new BaiIndexCache.



## [0.23.1] - 2019-03-21



### Added

 - Streamable BamReader (via stdin).

 - Enabled range-for on BamReader, compatible with the other *Query inputs.



## [0.23.0] - 2019-03-11



### Added

bamboo_build.sh

+1 −1
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@@ -45,7 +45,7 @@ unset BOOST_LIBRARYDIR 


# in order to make shared libraries consumable

# by conda and other package managers

export LDFLAGS="-static-libstdc++ -static-libgcc"

export LDFLAGS=${LDFLAGS:-"-fuse-ld=gold -static-libstdc++ -static-libgcc"}



source scripts/ci/setup.sh

source scripts/ci/build.sh

docs/source/conf.py

+2 −2
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@@ -103,9 +103,9 @@ author = u'Derek Barnett' 
# built documents.

#

# The short X.Y version.

version = '0.23.0'

version = '1.0.6'

# The full version, including alpha/beta/rc tags.

release = '0.23.0'

release = '1.0.6'



# The language for content autogenerated by Sphinx. Refer to documentation

# for a list of supported languages.

include/meson.build

+28 −2
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@@ -7,6 +7,7 @@ if not meson.is_subproject() 
    files([

      'pbbam/Accuracy.h',

      'pbbam/AlignmentPrinter.h',

      'pbbam/BaiIndexCache.h',

      'pbbam/BaiIndexedBamReader.h',

      'pbbam/BamFile.h',

      'pbbam/BamFileMerger.h',
@@ -20,6 +21,9 @@ if not meson.is_subproject() 
      'pbbam/BamTagCodec.h',

      'pbbam/BamWriter.h',

      'pbbam/BarcodeQuery.h',

      'pbbam/BgzipFastaWriter.h',

      'pbbam/BgzipFastqWriter.h',

      'pbbam/BgzipWriter.h',

      'pbbam/Cigar.h',

      'pbbam/CigarOperation.h',

      'pbbam/ClipType.h',
@@ -31,6 +35,7 @@ if not meson.is_subproject() 
      'pbbam/DataSetTypes.h',

      'pbbam/DataSetXsd.h',

      'pbbam/EntireFileQuery.h',

      'pbbam/FaiIndex.h',

      'pbbam/FastaCache.h',

      'pbbam/FastaReader.h',

      'pbbam/FastaSequence.h',
@@ -39,16 +44,19 @@ if not meson.is_subproject() 
      'pbbam/FastqReader.h',

      'pbbam/FastqSequence.h',

      'pbbam/FastqWriter.h',

      'pbbam/FormatUtils.h',

      'pbbam/FrameEncodingType.h',

      'pbbam/Frames.h',

      'pbbam/GenomicInterval.h',

      'pbbam/GenomicIntervalQuery.h',

      'pbbam/IFastaWriter.h',

      'pbbam/IFastqWriter.h',

      'pbbam/IndexedBamWriter.h',

      'pbbam/IndexedFastaReader.h',

      'pbbam/IndexedFastqReader.h',

      'pbbam/Interval.h',

      'pbbam/IRecordWriter.h',

      'pbbam/LocalContextFlags.h',

      'pbbam/MakeUnique.h',

      'pbbam/MD5.h',

      'pbbam/MoveAppend.h',

      'pbbam/Orientation.h',
@@ -73,11 +81,14 @@ if not meson.is_subproject() 
      'pbbam/SamTagCodec.h',

      'pbbam/SamWriter.h',

      'pbbam/SequenceInfo.h',

      'pbbam/SNR.h',

      'pbbam/Strand.h',

      'pbbam/StringUtilities.h',

      'pbbam/SubreadLengthQuery.h',

      'pbbam/Tag.h',

      'pbbam/TagCollection.h',

      'pbbam/TextFileReader.h',

      'pbbam/TextFileWriter.h',

      'pbbam/Unused.h',

      'pbbam/Validator.h',

      'pbbam/ZmwGroupQuery.h',
@@ -86,6 +97,22 @@ if not meson.is_subproject() 
      'pbbam/ZmwTypeMap.h']),

    subdir : 'pbbam')



  install_headers(

    files([

      'pbbam/bed/BedReader.h',

      'pbbam/bed/BedWriter.h']),

    subdir : 'pbbam/bed')



  install_headers(

    files([

      'pbbam/ccs/CCSHeader.h',

      'pbbam/ccs/CCSPbiBuilder.h',

      'pbbam/ccs/CCSRecord.h',

      'pbbam/ccs/CCSRecordFormat.h',

      'pbbam/ccs/CCSRecordReader.h',

      'pbbam/ccs/CCSRecordWriter.h']),

    subdir : 'pbbam/ccs')



  install_headers(

    files([

      'pbbam/exception/BundleChemistryMappingException.h',
@@ -100,7 +127,6 @@ if not meson.is_subproject() 
      'pbbam/internal/DataSetBaseTypes.h',

      'pbbam/internal/DataSetElement.h',

      'pbbam/internal/DataSetElement.inl',

      'pbbam/internal/Interval.inl',

      'pbbam/internal/PbiBasicTypes.inl',

      'pbbam/internal/PbiFilter.inl',

      'pbbam/internal/PbiFilterTypes.inl',