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Commits on Oct 22, 2024

• .github/workflows/ubuntu-builds.yml: fixing the name of the workflow

  andrewdavidsmith

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• Makefile.am: ensuring that the BAM-related sources are only used if --enable-hts is specified to configure

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Commits on Oct 21, 2024

• Adding ubuntu builds workflow

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Commits on Oct 20, 2024

• src/load_data_for_complexity.hpp: making forgotten change to type of rng seed in declaration of functions to load coverage counts

  andrewdavidsmith

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• Merge pull request #78 from smithlabcode/submodule-update

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• .github/workflows/cppcheck.yml: found cppcheck

  andrewdavidsmith

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• .github/workflows/cppcheck.yml: trying to find cppcheck

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• clang-format

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• Removing the unused srand with pid and time because it was never used in initializing the mt19937 which was generating randoms

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• only writing histograms to files and this is separate from verbose

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• cppcheck.yml: adding workflow for cppcheck

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• .cppcheck_suppress: adding newline before eof

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• .github/workflows/cpplint.yml: removing the step of checking version

  andrewdavidsmith

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• src/load_data_for_complexity.cpp: removing some unused variables

  andrewdavidsmith

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• src/bam_record_utils.cpp: fixing some issues from cppcheck including failing to throw an exception that was constructed

  andrewdavidsmith

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• src/bam_record_utils.hpp: fixing the use of bool values in less-than comparison

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• src/continued_fraction.hcpp: removing an unused function

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• .cppcheck_suppress: adding a config file for cppcheck

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• Collapsing consecutive verbose conditions and factoring a big chunk of verbose printing into a function from bound_pop

  andrewdavidsmith

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• src/continued_fraction.hpp: removing the return_degree function as it was never used

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• src/moment_sequence.cpp: removing the ACCEPT_HANKEL variable because although it was used in a condition and set both true and false in different places, when it was set to false a return always ha…

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• src/moment_sequence.cpp: fixing a var shadowing earlier var, adding const to args for LU_determinant

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• src/to-mr.cpp: removing this file as its only remaining functionality has now been included in gc_extrap with BAM input

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Commits on Oct 19, 2024

• src/load_data_for_complexity.cpp: satsifying cpplint

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• src/pop_size.cpp: providing option to report histogram to a file

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• src/bound_pop.cpp: providing option to report histogram to a file

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• src/gc_extrap.cpp: merging option to report the 'about' information with the no args help

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• src/lc_extrap.cpp: merging option to report the 'about' information with the no args help

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• src/load_data_for_complexity.cpp: removing some code that was aimed at eliminating a memory leak that turned out not to exist anyway

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• src/load_data_for_complexity.cpp: fixed the priority queue which was sorting in the wrong direction

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• src/lc_extrap.cpp: moving the report_histogram function to common

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• src/gc_extrap.cpp: adding the ability to output the counts histogram

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• src/c_curve.cpp: adding the ability to output the counts histogram

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• src/load_data_for_complexity.cpp: fixing a bug in setting endpoints of genomic intervals from BAM records

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• src/common.hpp: adding the report_histogram to the common sources

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