Original duplicates now built-in without needing special build args - #112

Merged

andrewdavidsmith merged 29 commits into

mainfrom

original-dups-init-performance

Aug 12, 2026

Commits on Aug 11, 2026

src/bam_file.hcpp: adding a function to pre-load the duplication counts
andrewdavidsmith
committed
a632829
src/fastq_bgzf_file.hcpp: adding a function to pre-load the duplication counts
andrewdavidsmith
committed
325663a
src/results_collector.hpp: adding a mode to initialize a results_collector when duplication words to be counted need to be initialized for original dups
andrewdavidsmith
committed
4cde64d
src/original_duplicates.hcpp: adding sources to control initialization of duplicates to count in original duplicates mode
andrewdavidsmith
committed
57967f5
src/quality_score.hcpp: adding missing includes
andrewdavidsmith
committed
ca1b6ca
src/run_mode.hcpp: added a run mode setting for original dups
andrewdavidsmith
committed
da86403
src/duplication_results.hcpp: keeping most code that works for original dups alongside new dups analysis method; aiming to have both side-by-site
andrewdavidsmith
committed
2c49bff
src/results_summary.hcpp: removing things that depend both on the preprocesser var ORIGINAL_DUPS and keeping both code side-by-site
andrewdavidsmith
committed
e9c4556
CMakeLists.txt: adding object for the original_duplicates source
andrewdavidsmith
committed
4fdd8e4
src/results_collector.hpp: initialization in the init function based on run_mode for original_dups
andrewdavidsmith
committed
ea9c6a1
src/falco_analyzer.hcpp: adding dups_init argument to analyze function purely to facilitate original_dups mode and moving the initialization of results_collector objects per thread into the threads…
andrewdavidsmith
committed
3610e2a
src/results_collector.hpp: building original_dups directly into the analysis with a flag; performance uncertain
andrewdavidsmith
committed
4ec0ceb
src/duplication_results.hcpp: removing preprocessor flags for original dups analysis
andrewdavidsmith
committed
a394f41
src/falco.cpp: adding code and cli options for user to specify original dups mode without building for it
andrewdavidsmith
committed
1401ba4
README.md: updates related to changes for original duplication results
andrewdavidsmith
committed
896c0fb

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Original duplicates now built-in without needing special build args - #112

Original duplicates now built-in without needing special build args#112
andrewdavidsmith merged 29 commits into
mainfrom
original-dups-init-performance

Commits on Aug 11, 2026

src/bam_file.hcpp: adding a function to pre-load the duplication counts

src/fastq_bgzf_file.hcpp: adding a function to pre-load the duplication counts

src/results_collector.hpp: adding a mode to initialize a results_collector when duplication words to be counted need to be initialized for original dups

src/original_duplicates.hcpp: adding sources to control initialization of duplicates to count in original duplicates mode

src/quality_score.hcpp: adding missing includes

src/run_mode.hcpp: added a run mode setting for original dups

src/duplication_results.hcpp: keeping most code that works for original dups alongside new dups analysis method; aiming to have both side-by-site

src/results_summary.hcpp: removing things that depend both on the preprocesser var ORIGINAL_DUPS and keeping both code side-by-site

CMakeLists.txt: adding object for the original_duplicates source

src/results_collector.hpp: initialization in the init function based on run_mode for original_dups

src/falco_analyzer.hcpp: adding dups_init argument to analyze function purely to facilitate original_dups mode and moving the initialization of results_collector objects per thread into the threads…

src/results_collector.hpp: building original_dups directly into the analysis with a flag; performance uncertain

src/duplication_results.hcpp: removing preprocessor flags for original dups analysis

src/falco.cpp: adding code and cli options for user to specify original dups mode without building for it

README.md: updates related to changes for original duplication results

Commits on Aug 12, 2026

data/test_scripts/orig_dups.sh: adding a test for original duplications mode

README.md: update to readme

cmake/tests.cmake: adding a test for original duplicates

data/test_data/md5sum.txt: adding an output hash for original duplicates

src/bam_file.cpp: bugfix where revcomp wasn't taken for reverse strand reads when identifying the duplication set for original duplicates

src/duplication_results.hcpp: iwyu

src/falco_analyzer.hcpp: iwyu

src/original_duplicates.hcpp: iwyu

src/fastq_bgzf_file.hcpp: iwyu

src/falco.cpp: clang-tidy not understanding a partial move-from

src/duplication_results.hpp: type consistency for count_at_limit

src/original_duplicates.cpp: nolint for an empty loop variable

CMakeLists.txt: adding a forgotten dependency

src/fastq_bgzf_file.cpp: changing the n_unique_multiplier to match the one in bam_file and likely it's too large. If we hit 2x then we know the duplication should fail