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Correct pileup motif ownership, validation, and mask limits #702

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Correct pileup motif ownership, validation, and mask limits #702

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983f0f1
fix: make pileup motif lookup interval invariant
SuhasSrinivasan Aug 6, 2026
95fca22
Reject negative combine-strand motif displacement
SuhasSrinivasan Aug 5, 2026
678c5b0
test: cover combine-strand motif validation ordering
SuhasSrinivasan Aug 6, 2026
f870d70
fix: validate combine-strand motifs before output
SuhasSrinivasan Aug 6, 2026
048b285
test: bound dense combined motif scan work
SuhasSrinivasan Aug 6, 2026
eb5fe27
fix: bound combined motif closure scans
SuhasSrinivasan Aug 6, 2026
ea33168
Reject pileup motif counts above mask capacity
SuhasSrinivasan Aug 11, 2026
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9 changes: 6 additions & 3 deletions book/src/advanced_usage.md
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Expand Up @@ -269,9 +269,12 @@ Modified Base Options:
is used, the resulting output BED file will indicate the motif in the
"name" field as <mod_code>,<motif>,<offset>. For example, given
`--motif CGCG 2 --motif CG 0` there will be output lines with name
fields such as "m,CG,0" and "m,CGCG,2". To use this option with
`--combine-strands`, all motifs must be reverse-complement palindromic
or an error will be raised.
fields such as "m,CG,0" and "m,CGCG,2". At most eight motifs are
supported, including motifs added by `--cpg` or `--modified-bases`.
To use `--combine-strands`, exactly one motif must be supplied. It
must be reverse-complement palindromic, and the reverse-strand anchor
must not precede the forward-strand anchor, or an error will be
raised.

--cpg
Only output counts at CpG motifs
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7 changes: 5 additions & 2 deletions book/src/intro_pileup.md
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Expand Up @@ -141,8 +141,11 @@ oligo_741_adapters 39 40 m,CG,0 4 - 39 40 255,0,0 4 100.00 4 0 0 0 0 0 0
oligo_741_adapters 39 40 m,CGCG,2 4 - 39 40 255,0,0 4 100.00 4 0 0 0 0 0 0
```

The `--combine-strands` flag can be combined with `--motif` however all motifs must be reverse-complement palindromic (`CG` _is_ a palindrome but `CHH` is not).
Only one motif at a time is supported with `--combine-strands` is used (see [limitations](./limitations.md) for details).
Pileup supports at most eight motifs, including motifs added by `--cpg` or `--modified-bases`.

The `--combine-strands` flag requires exactly one motif, supplied with `--motif` or `--cpg`, and that motif must be reverse-complement palindromic (`CG` _is_ a palindrome but `CHH` is not).
The reverse-strand anchor must not precede the forward-strand anchor; for example, `--motif CGCG 0 --combine-strands` is supported, while `--motif CGCG 2 --combine-strands` is not currently supported.
See [limitations](./limitations.md) for more details.

## Partitioning reads based on phasing information with `--phased`

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