Adding flag to format command for reads in SAM orientation#278

Merged

andrewdavidsmith merged 7 commits intomasterfrom

sam-orientation-for-format

Jul 20, 2025

Commits on Jul 20, 2025

Makefile.am configure.ac: assigning CXXFLAGS only if the user didn't specify anything and moving the assignment to configure.ac from Makefile.am
andrewdavidsmith
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src/common/bam_record_utils.hcpp: adding a function revcomp_qseq to allow for reverse complementing the read sequence without changing the flags
andrewdavidsmith
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src/common/dnmtools_utils.hcpp: cleaning up the code
andrewdavidsmith
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src/utils/format-reads.cpp: adding a flag to accept reads that are in strict SAM format with the reverse complement qseq when the read maps to the negative strand. Also cleaning up the code
andrewdavidsmith
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data/md5sum.txt: updating hash for output of format command
andrewdavidsmith
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data/md5sum.txt: updating hash for output of uniq command
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src/abismal: updating submodule
andrewdavidsmith
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