Fix copy-pasted UMI help text on paired-guide --pg-* options (#22) - #24
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The count help for --pg-start/--pg-end/--pg-start-2/--pg-end-2 was copied verbatim from the UMI options: it read "position of UMI ... if UMI is found on the first/second pair" and its examples referenced --umi-start/--umi-end, implying a UMI is required for paired-guide counting. It is not. Rewrite the four strings to describe the second guide and the correct coordinate reference for each mode: --pg-start/--pg-end are measured from the end of the first guide (--pairguide firstpair), and --pg-start-2/--pg-end-2 from the first nucleotide of read 2 (--pairguide secondpair), matching the actual slices in mageckcount_processonefile. Also correct --pg-min-read help, which said "Default 2" while the default is 3. Reported in issue #22. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EZcdrQdWJfczuqaMeZ3DBD
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Closes #22.
The
counthelp text for the paired-guide options--pg-start,--pg-end,--pg-start-2, and--pg-end-2was accidentally copied verbatim from the UMI options. It read "The relative start/end position of UMI ... if UMI is found on the first/second pair" and its worked examples referenced--umi-start/--umi-end— which reads as though a UMI is required to count paired-guide screens. It is not (reported in #22).What changed
--pg-*help strings to describe the second guide and the correct coordinate reference for each mode, matching the actual code inmageckcount_processonefile:--pg-start/--pg-end— measured from the end of the first guide (--pairguide firstpair); slice isfseq[(end_1st_guide)+pg_start : (end_2nd_guide)+pg_end].--pg-start-2/--pg-end-2— measured from the first nucleotide of read 2 (--pairguide secondpair); slice isfseq1[pg_start_2 : pg_end_2].--pg-min-readhelp, which stated "Default 2" while the actual default is3.Docs-only / help-string change; no behavior change. A companion PR updates the generated
USAGE.mdindavidliwei/mageck2-doc.