IUPAC symbols for orig-dups mode: non-ACGT (case insensitive) are converted to N by andrewdavidsmith · Pull Request #147 · smithlabcode/falco

src: grade adapter, overrepresented, N content and duplication as FastQC

MaximilianStammnitz

authored and

andrewdavidsmith

committed

a143908

src: added my initials/email to the comments blocks for the grading fix

MaximilianStammnitz

authored and

andrewdavidsmith

committed

a2a29ed

update comments

MaximilianStammnitz

authored and

andrewdavidsmith

committed

e34c187

src/original_duplicates.cpp: moving code to initialize original duplicates analysis here

andrewdavidsmith

committed

9c12e93

src/fastq_bgzf_file.hcpp and src/bam_file.hcpp: moving code for initializing original duplication data structures to original_duplicates.cpp

andrewdavidsmith

committed

d798f58

src/original_duplicates.cpp: adding forgotten headers

andrewdavidsmith

committed

260869f

src/original_duplicates.cpp: adding to_acgtn in both the init_orig_dups_bam and init_orig_dups_fq to convert all non-ACGT letters to N prior to forming a falco_word when initializing the unique 're…

andrewdavidsmith

committed

bbd4785

CMakeLists.txt: original_duplicates object links to HTSLIB so that the htslib headers will be visibile when making original_duplicates.o

andrewdavidsmith

committed

87bfa4c

src/original_duplicates.cpp: fix changing transform to for_each_n when complementing the already reversed read sequence for revcomp mappers

andrewdavidsmith

committed

d38c6a4

static analysis

andrewdavidsmith

committed

24c9995

Merge branch 'fix-iupac-issue-for-orig-dups' of github.com:smithlabcode/falco into fix-iupac-issue-for-orig-dups

andrewdavidsmith

committed

331b0ce

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IUPAC symbols for orig-dups mode: non-ACGT (case insensitive) are converted to N - #147

IUPAC symbols for orig-dups mode: non-ACGT (case insensitive) are converted to N#147
andrewdavidsmith merged 23 commits into
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fix-iupac-issue-for-orig-dups

Commits on Nov 2, 2026

src/original_duplicates.cpp: moving code to initialize original duplicates analysis here

src/fastq_bgzf_file.hcpp and src/bam_file.hcpp: moving code for initializing original duplication data structures to original_duplicates.cpp

src/original_duplicates.cpp: adding forgotten headers

src/original_duplicates.cpp: adding to_acgtn in both the init_orig_dups_bam and init_orig_dups_fq to convert all non-ACGT letters to N prior to forming a falco_word when initializing the unique 're…

CMakeLists.txt: original_duplicates object links to HTSLIB so that the htslib headers will be visibile when making original_duplicates.o

src/original_duplicates.cpp: fix changing transform to for_each_n when complementing the already reversed read sequence for revcomp mappers

static analysis

Commits on Nov 9, 2026

src: grade adapter, overrepresented, N content and duplication as FastQC

src: added my initials/email to the comments blocks for the grading fix

update comments

src/original_duplicates.cpp: moving code to initialize original duplicates analysis here

src/fastq_bgzf_file.hcpp and src/bam_file.hcpp: moving code for initializing original duplication data structures to original_duplicates.cpp

src/original_duplicates.cpp: adding forgotten headers

src/original_duplicates.cpp: adding to_acgtn in both the init_orig_dups_bam and init_orig_dups_fq to convert all non-ACGT letters to N prior to forming a falco_word when initializing the unique 're…

CMakeLists.txt: original_duplicates object links to HTSLIB so that the htslib headers will be visibile when making original_duplicates.o

src/original_duplicates.cpp: fix changing transform to for_each_n when complementing the already reversed read sequence for revcomp mappers

static analysis

Merge branch 'fix-iupac-issue-for-orig-dups' of github.com:smithlabcode/falco into fix-iupac-issue-for-orig-dups

Commits on Nov 10, 2026

data/test_scripts/iupac_dups.sh: adding tests for dups with iupac symbols ensuring all are treated like N

cmake/tests.cmake: adding tests for IUPAC symbols and duplicates ensuring all non-ACGT are treated like N

data/test_data/md5sum.txt: adding test hashes

data/test_data/iupac_dups.fq.gz: adding test data file for iupac when running in orig-dups mode

data/test_scripts/iupac_dups.sh: fixing typo