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Commits on Nov 8, 2014
  1. Merge pull request #368 from broadinstitute/intel_individual_field_va…

    MauricioCarneiro committed Nov 8, 2014
    …lue_iterator_increment
    
    Void return type for operator ++ and -- in IndividualFieldValueIterator
  2. Merge pull request #369 from broadinstitute/dr_fix_genotype_encoding_…

    MauricioCarneiro committed Nov 8, 2014
    …of_vector_ends
    
    Prevent vector end values from getting transformed during Genotype encoding, and detect invalid values
  3. Merge pull request #370 from broadinstitute/jt_rbs_updates

    MauricioCarneiro committed Nov 8, 2014
    A few small changes through the Ref Block Spilt stack
Commits on Nov 6, 2014
  1. Merge pull request #356 from broadinstitute/dr_refactor_variant_to_us…

    MauricioCarneiro committed Nov 6, 2014
    …e_variantheader
    
    Eliminate duplication of VariantHeader functionality in Variant class
Commits on Nov 4, 2014
  1. Merge pull request #353 from broadinstitute/mc_travis_update_cmake

    MauricioCarneiro committed Nov 4, 2014
    Travis: add prebuilt cmake 3.1
  2. Travis: add prebuilt cmake 3.1

    MauricioCarneiro committed Nov 4, 2014
    * update the commented out code that was only for 2.8.7
  3. Merge pull request #352 from nsubtil/cmake-fixes

    MauricioCarneiro committed Nov 4, 2014
    CMake fixes for Firepony
Commits on Nov 2, 2014
  1. Make CMAKE the default build script

    MauricioCarneiro committed Nov 2, 2014
    * use add_compile_options instead of hardcode setting of the env variable
    * remove lib from include directories
    * add header files to the source list
    * include htslib directories at the cmake build location (no longer using the git-submodule)
    * remove git submodule and use htslib via cmake from now on.
    * exclude tests from building by default
    * build release by default, but tests in debug mode
    * remove boost build files
    * add cmake to travis
    * add release / debug options to the build
    * add run_test option for building and running tests in one command
Commits on Oct 31, 2014
  1. Merge pull request #345 from broadinstitute/dr_rev_htslib_and_remove_…

    MauricioCarneiro committed Oct 31, 2014
    …synced_reader_hack
    
    Rev htslib to be in sync with our fork, and remove ugly hack from SyncedVariantReader
  2. Merge pull request #337 from broadinstitute/dr_fix_additional_reader_…

    MauricioCarneiro committed Oct 31, 2014
    …segfaults_on_nonexistent_files
    
    Handle file/index not found errors in reader classes gracefully instead of segfaulting!
Commits on Oct 29, 2014
  1. Merge pull request #329 from broadinstitute/mc_cmake_clion

    MauricioCarneiro committed Oct 29, 2014
    First attempt at a CMAKE build system
  2. Address @nsubtil comments on code-review

    MauricioCarneiro committed Oct 29, 2014
    * move find packages to root CMakeLists.txt
    * swtich add->definitions to target_compile_definitions
    * add variant builder files to the project
  3. First attempt at a CMAKE build system

    MauricioCarneiro committed Oct 27, 2014
    now we can build gamgee and run tests. It all works on CLION!!!!
Commits on Oct 26, 2014
  1. Merge pull request #301 from broadinstitute/jt_mvr_fixes

    MauricioCarneiro committed Oct 26, 2014
    Store all variant headers and also combine them for an overall header
Commits on Oct 15, 2014
  1. Merge pull request #313 from broadinstitute/ak_ignore_emacs_temporaries

    MauricioCarneiro committed Oct 15, 2014
    ignore emacs temporary files
Commits on Oct 14, 2014
  1. Merge pull request #294 from broadinstitute/db_read_groups

    MauricioCarneiro committed Oct 14, 2014
    ReadGroup class along with some support in SamHeader.
  2. Merge pull request #309 from broadinstitute/mc_remove_ycm_files

    MauricioCarneiro committed Oct 14, 2014
    Remove ycm extra configuration files
  3. Merge pull request #312 from broadinstitute/ak_fix_samples_to_include…

    MauricioCarneiro committed Oct 14, 2014
    …_in_variant_reader
    
    fix for forgotten list of samples to include
Commits on Oct 2, 2014
  1. Merge pull request #291 from broadinstitute/mc_relase_mode_testing

    MauricioCarneiro committed Oct 2, 2014
    Travis: run tests in release mode in master only
  2. Travis: run tests in release mode in master only

    MauricioCarneiro committed Sep 29, 2014
    create a new *production* mode to eliminate the -finline-functions that
    is no longer supported by clang 3.5
    
    also create a global fixture for initialization of global variables in
    the variant reader test.
    
    closes #290
Commits on Sep 29, 2014
  1. Merge pull request #275 from broadinstitute/mc_snps_and_indels

    MauricioCarneiro committed Sep 29, 2014
    Genotype: add convenience functions: snp, indel...
  2. Genotype: add convenience functions: snp, indel...

    MauricioCarneiro committed Sep 24, 2014
    This is a tricky request from Louis which I anticipate to be a big hit
    with the compbios. Everyone wants to query directly at the genotype what
    kind of event it is. The problem is that doing so is expensive. One
    should always strive to batch this kind of computation across all
    samples using functionality like select_if or simple for_each loops.
    
    However sometimes you want to just query one or two of these conditions
    and it is nice to have such convenience functions. I strived here to
    achieve as much performance as possible without increasing the state of
    the Genotype object. To avoid string comparisons, all member functions
    rely on an AlleleMask that pre-computes the string differences in the
    alt/ref fields only once. All functions operate on key comparisons only.
    
    Still, if you are going to use this for multiple comparisons such as:
    
    ```c++
    if (genotype.insertion() || genotype.snp() && genotype.simple())
      do_something(genotype);
    ```
    
    You will most likely be better off writing your own for loop instead of
    paying for 3 passes on the data. But for quick queries in data with few
    alleles (like diploids) this should be fine.
    
    closes #204
Commits on Sep 26, 2014
  1. Merge pull request #288 from broadinstitute/jt_move_field_type

    MauricioCarneiro committed Sep 26, 2014
    Move the field_type checks to VariantHeader
  2. Merge pull request #281 from broadinstitute/mc_travis_experiments

    MauricioCarneiro committed Sep 26, 2014
    Travis: add precompiled packages for our tools
  3. Travis: add precompiled packages for our tools

    MauricioCarneiro committed Sep 25, 2014
    * add doxygen 1.8 binary package
    * add clang-3.5 + clang modernize
    * add gcc 4.9
    
    I also have a boost package compiled with gcc 4.9 but the current clang
    package depends on gcc 4.8 (for stdlibc++) and resolving this was a
    dependency nightmare that I decided to postpone. Boost-155 is currently
    being used from a PPA.
    
    I also added clang-format and clang-modernize #56 but I will only close
    that item when we actually use them in the build process. It's available
    now.
    
    closes #57
Commits on Sep 25, 2014
  1. Merge pull request #280 from broadinstitute/jt_tsca_tiling_const

    MauricioCarneiro committed Sep 25, 2014
    Mark tsca_tiling as const
  2. Merge pull request #279 from broadinstitute/jt_gamgee_h

    MauricioCarneiro committed Sep 25, 2014
    Add reference_iterator.h and reference_map.h
  3. Merge pull request #278 from broadinstitute/lb_277_move_interval_chan…

    MauricioCarneiro committed Sep 25, 2014
    …ges_to_gamgee
    
    Copied str method from foghorn interval
Commits on Sep 24, 2014
  1. Merge pull request #272 from broadinstitute/mc_banish_all_const_membe…

    MauricioCarneiro committed Sep 24, 2014
    …r_variables
    
    Banish all const member variables
  2. Banish all const member variables

    MauricioCarneiro committed Sep 24, 2014
    They prevent move operations and really make no sense. If you need to
    make an object immutable, make *it* const, not it's member variables. If
    you need a class that producess immutable objects, use another design
    pattern.
    
    closes #271
  3. Merge pull request #270 from broadinstitute/mc_expunge_copy_then_move

    MauricioCarneiro committed Sep 24, 2014
    Expunge the copy-then-move idiom