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CHANGELOG
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CHANGELOG
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= SeqAn Changelog =
Add a new list item '''AT THE TOP''' for each change (excluding trivial things like changes to whitespace and comments).
Link to changsets with `[CHANGESET-NUMBER]` and tickets with `#TICKET-NUMBER` whenever possible.
You can use Trac wiki syntax.
== Trunk ==
* ''config.h'' and generated forward files are now created in the build directory.
* Removing basic_definition.h, moving contents into basic_metaprogramming, basic_tag and new basic_math.h.
* Documentation of Simple Holder.
* Cleanup of Holder header, removing unused, undocumented, untested Tristate2 holder.
* Documentation for Hosted Object Concept.
* Documentation for metafunctions.
* Documentation for `SEQAN_ENABLE_PARALLELISM`.
* Adding support for documenting enums and macros to dddocs.
* Fixing wrong usage line displayed in Mason read simulator.
* Removing unused, undocumented `SinglePool2` and `ChunkPool2` allocators.
* Cleaning up allocator headers.
* Cleaned up iterator infrastructure a bit.
* Cleaned up various headers in basic module, added documentation for `ProfileType` class.
* Cleanup of ''basic_proxy.h'' header, making `Proxy` a `class` instead of a `struct`.
* Removing empty ''basic_operator.h''.
* Removing `VoidHolder<>`, in ''basic_holder_dynamic.h''.
* Documentation and cleanup of `LogValue<>`.
* Documentation for `VolatilePtr<>`.
* Removing ''basic_counted_ptr.h'' that contained only unused code.
* Did some renaming of debugging/testing assertion macros.
* `SEQAN_ASSERT_TRUE` is now called `SEQAN_ASSERT` (`SEQAN_ASSERT_TRUE_MSG` is now `SEQAN_ASSERT_MSG`).
* The old `SEQAN_ASSERT` macro from old testing/debugging system has been removed, along with the `SEQAN_CHECK*`, `SEQAN_REPORT`, `SEQAN_DO*` macros.
* The only remaining part from the old test system are the internal functions `_compareBinaryFiles()`, `_compareTextFilesReadChar()`, `_compareTextFiles()`.
* The assertion macros have been replaced in the library and SeqAn applications.
* Adding functions `isBitSet()`, `clearBit()`, `clearAllBits()`, `setBitTo()`, `setBit()` to misc header ''misc_bit_twiddling.h''.
* Adding Union-Find data structure in `misc/misc_union_find.d`.
* fixing `eraseBack()` with block strings.
* Using Union-Find data structure in Kruskal's algorithm to improve the running time to `O(m log m)`.
* Changed `resizeVertexMap` and `resizeEdgeMap`. The two-parameter versions have similar semantics as before and initialize the map with 0. The three-parameter versions expect an additional "prototype version" that is copied/assigned into the map. The old copy-from-arrayy versions are now called `assignVertexMap` and `assignEdgeMap`. Also updated the tutorial.
* Adding documentation of graph iterator constructors.
* Adding full segment support for journaled strings, including segment assignment, e.g. `infix(journaledString, 0, 10) = DnaString("CGAT")`.
* Adding `position()`, `operator-()`, `operator[]` with proxy functionality and relation operators to journaled string iterator.
* Adding metafunction `GetDefaultRng<T>::Type` and function `defaultRng()` for construction of global random number generators to be used by default in randomized data structures and algorithms.
* Adding specialization of Uniform probability density function for `bool`s and tests.
* Documented `getQuality`.
== Release 1.2 ==
* Splitting file ''sequence_multiple.h'' into ''string_set*.h'', ''iter_concat_virtual.h'', and ''sequence_concatenator.h''.
* Bound check in `iter()`.
* Adding `SEQAN_IS_64_BIT` and `SEQAN_IS_64_BIT` macros, defined to either `0` or `1`, depending on the platform.
* Adjusting `MUM` and `MEM` to new naming schema. (#836)
* Adding `SEQAN_OMP_PRAGMA` to hide `#pragma omp` when not compiling with OpenMP to suppress warnings. (#353)
* The test system deletes all files with the same name as temporary file names generated during the tests. (#377)
* Adding documentation for the alphabets `Dna5Q` and `DnaQ` which allow to store 5/4 nucleotides along with the quality in one byte (`char`).
* Defining integer types (__int8, __uint8, ...) for MinGW, too.
* Making snp_store compile with LLVM.
* Removing type `Byte` since it clashes with zlib (#843). Note that the types `Ascii` and `Unicode` are deprecated and will be removed soon (#849).
* Fixing a bug in `iter()` with iterator (#848).
* Adding module '''parallel''', bootstrapping with atomic primitives and atomic `min()`/`max()` functions, fully tested.
* Slightly optimized assign for strings when source and target are empty.
* Slightly optimized `empty()` for strings.
* Fixing problem with MaxValue<>, MinValue<> of RNG with multiple compilation units.
* Also defining `std::swap` for strings and string sets.
* Fixing bug in `windowFindNext()`.
* Setting flags for RelDebug build type correctly for apps.
* Removed unused and undocumented `string_value_expand.h` / `String<TValue, ValueExpand<...> >`
* Various comment / formatting / documentation changes and annotations in sequence module.
* Renaming `string_stack.h` to `string_block.h` and adding header field for author.
* Adding comment about value expand string, also see #839.
* Renaming `lexical.h` to `sequence_lexical.h` adding note on the location of `ordValue`, also see #838.
* Renaming `string_pointer.h` to `adapt_array_pointer.h` and adding some notes for issues to review, e.g. #837.
* Improving coding style compliance of Array String implementation.
* Making documentation about assigning to CStyle SeqAn strings more clear, adjusting comments.
* Documenting `reAlign()`, various small comment and whitespace fixes in consensus module.
* Comparison operator for tag selector.
* Experimental BAM reading/writing.
* Allowing the store elements of fragment stores to be comparable.
* Adding bundled version of ''samtools''.
* Fixing documentation for `resize()`, `reAlign()`, `reverse()`, and `score()`.
* Fixing `lowerBoundAlignedReads()` and `lowerBoundAlignedReads()` when searching by begin and end position.
* Properly documenting `lowerBoundAlignedReads()` and `upperBoundAlignedReads()`.
* Fixing documentation about include for ''misc/misc_cmdparser.h'', was ''seqan/misc.h'', corrected to ''seqan/misc/misc_cmdparser.h''.
* Assertion in semiglobal SWIFT finder that hits begin <= end.
* Initializing state.errors in Myers Ukkonen banded pattern initialization.