Code

Several major updates#78

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andrewdavidsmith merged 58 commits intomastersmithlabcode/preseq:masterfrom submodule-updatesmithlabcode/preseq:submodule-updateCopy head branch name to clipboardOct 20, 2024

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Commits on Oct 18, 2024

• src/smithlab_cpp: updating submodules

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• Fixing hashes on test outputs and fixing script for testing lc_extrap

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• src/moment_sequence.hcpp: removing unused verbose arguments to functions

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• src/c_curve.cpp: removed code that was not used for c_curve from this file

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• src/load_data_for_complexity.hcpp: made filenames pass by const reference and moved the code dealing with htslib stuff down to the bottom of the source file

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• src/lc_extrap.cpp: removing c_str

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• src/gc_extrap.cpp: removing unused verbose arg to load_coverage_counts_MR function

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• src/bound_pop.cpp: removing unused verbose arg to quadrature rules functions

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• src/bamxx: Adding bamxx submodule

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• Makefile.am: removing the to-mr target and adding bamxx and src/bam_record_utils.hcpp as new dependent files

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• src/load_data_for_complexity.hcpp: Updating the function to load counts from BAM files for paired-end. This involves using both the tid and pos of the given read along with the tid and pos of its m…

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• Adding back functionality to work with BAM in paired-end mode now using bamxx and assuming that mates are identified using the mtid and mpos values within the BAM record

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• src/common.hcpp: adding these files

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• src/bam_record_utils.hcpp: adding these source file

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• src/dnmt_error.hpp: adding this file because bam_record_utils.cpp needs it

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• Formatting with clang-format and linting with cpplint

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Commits on Oct 19, 2024

• src/load_data_for_complexity.hpp: adding a function to load coverage counts for BAM input, which doesn't care about mate pairs

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• src/load_data_for_complexity.cpp: adding structs to gather data together, and eliminated a bunch of redundant code

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• src/gc_extrap.cpp: added functionality to do genome coverage from BAM format

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• Adding threads for functions that read BAM input

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• src/load_data_for_complexity.cpp: factoring out sorted order check on reads to an outer scope and adding a forgotten section of code to take care of the rest of the priority queue on sorted parts a…

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• src/load_data_for_complexity.cpp: linting with cpplint

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• src/load_data_for_complexity.cpp: fixing a bug in checking whether a read is mapped -- the condition was inverted

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• src/load_data_for_complexity.cpp: another bugfix related to checking for mapped reads

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• src/load_data_for_complexity.cpp: fixing a bug in checking sorted order of reads in BAM format

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• src/smithlab_cpp: updating submodule

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• src/load_data_for_complexity.cpp: formatting and comments

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• src/lc_extrap.cpp: adding code to format the histogram and write it to a file if selected on cli

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

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

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

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

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

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

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

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• src/load_data_for_complexity.cpp: satsifying cpplint

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Commits on Oct 20, 2024

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

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

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

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• .cppcheck_suppress: adding a config file for cppcheck

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• src/continued_fraction.hcpp: removing an unused function

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

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

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• src/load_data_for_complexity.cpp: removing some unused variables

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

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• .cppcheck_suppress: adding newline before eof

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• cppcheck.yml: adding workflow for cppcheck

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

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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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• clang-format

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

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

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