Allowing unmapped reads in counts, bsrate, format and uniq#261

Merged

andrewdavidsmith merged 4 commits intomasterfrom

allow-unmapped-reads-in-methcounts

May 13, 2025

Commits on May 12, 2025

src/analysis/methcounts.cpp: reporting tid along with error message for incorrect chrom sorting and skipping any unmapped reads which are identified by get_tid returning -1
andrewdavidsmith
committed

Commits on May 13, 2025

src/analysis/bsrate.cpp: skipping any reads in the input that are not mapped as indicated by a -1 for tid obtained by get_tid
andrewdavidsmith
committed
src/utils/format-reads.cpp: when processing reads to format, but not to check read names for a suffix to ignore, if the tid is found to be negative ignore the read as it is unmapped
andrewdavidsmith
committed
src/utils/uniq.cpp: skipping any unmapped reads which have tid -1 from the get_tid function
andrewdavidsmith
committed