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smithlabcode
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Minor bugfixes and improvements related to reading from stdin
- #125
#125
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andrewdavidsmith
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output-dir-name-fix-with-stdin
smithlabcode/falco:output-dir-name-fix-with-stdin
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Sep 9, 2026
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Minor bugfixes and improvements related to reading from stdin
#125
andrewdavidsmith
merged 10 commits into
main
smithlabcode/falco:main
from
output-dir-name-fix-with-stdin
smithlabcode/falco:output-dir-name-fix-with-stdin
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Commits
Commits on Sep 8, 2026
src/falco.cpp: when input is from stdin, the name given as positional arg and used as name for data set, is not modified by attemting to remove a filename extension, because the inputis not a file
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src/run_mode.hcpp: adding do_stdin to run_mode
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Commits on Sep 9, 2026
src/sam_stdin.cpp: adding very simple validation for SAM files that only applies to records, so after the header has been read or if there is no header
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src/fqrec.hpp: adding some constructors to keep other sources cleaner
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src/sam_stdin.cpp: fixing function signature for validate_sam
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src/fastq_stdin.cpp: updating instantiation of fq_task_t, fixing signature of validate_fastq and moving that validation to the analogous place as in sam_stdin
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src/fastq_file.cpp: simpler instantiation of fq_task_t for symmetry with how it's done for other classes
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src/falco.cpp: attempting to simplify surface-level logic related to setup that depends on whether input is from stdin, which is likely rare
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src/sam_stdin.cpp: adding forgotten header
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README.md: some minor updates
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