Adding flag to format command for reads in SAM orientation#278
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andrewdavidsmith merged 7 commits intomasterfrom Jul 20, 2025
Merged
Adding flag to format command for reads in SAM orientation#278andrewdavidsmith merged 7 commits intomasterfrom
andrewdavidsmith merged 7 commits intomasterfrom
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…specify anything and moving the assignment to configure.ac from Makefile.am
…llow for reverse complementing the read sequence without changing the flags
… strict SAM format with the reverse complement qseq when the read maps to the negative strand. Also cleaning up the code
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SAM orientation reverse complements reads that map to the negative strand. Abismal can now output in strict SAM format if a flag is given. This PR adds the functionality in the format command to accept the strict SAM format.