NOTICE

RapidMACS
Copyright (c) 2026 Ling-Hong Hung

RapidMACS is distributed under the MIT License (see LICENSE).

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Relationship to MACS3 — https://github.com/macs3-project/MACS
Copyright (c) 2008-2024, Tao Liu lab and contributors
BSD 3-Clause License
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MACS was originally developed in X. Shirley Liu's group; Tao Liu and the MACS3
contributors have maintained and extended it since. We are grateful for that
sustained work and for the permissive licence under which it is released.

RapidMACS reproduces the paired-end narrow peak-calling behaviour of
`macs3 callpeak` v3.0.3. It is an independent implementation, not a port:
it was written clean-room from MACS3's published algorithmic specification
and validated by comparing its outputs against MACS3 v3.0.3 reference
outputs. **No MACS3 code is included in this software**, in original or
translated form, and RapidMACS is not a derivative work of MACS3.

One behaviour could not be reconstructed from the specification alone: the
per-event `pos_array` that MACS3 iterates when selecting the median member of
a tied pileup maximum during summit calling. For that behaviour, and for
comparable low-level details needed to reach byte-for-byte output equivalence,
MACS3's openly available source was consulted to determine what the reference
implementation does. The resulting RapidMACS code
(`src/macs3_pos_array.cc`, `include/rapidmacs/macs3_pos_array.h`) was written
independently and documents the correspondence to MACS3's
`Pileup.quick_pileup` and `Pileup.se_all_in_one_pileup`.

This notice is an acknowledgement of MACS3 and of the reference behaviour
RapidMACS targets. It is not a claim that any part of this software is
licensed under, or encumbered by, the BSD 3-Clause License.

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htslib — https://github.com/samtools/htslib
Copyright (c) Genome Research Ltd. and contributors
MIT/Expat License
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RapidMACS links against htslib for the Poisson tail routines in `kfunc.h` and
for BAM I/O. htslib is referenced as a git submodule under
`third_party/htslib` (pinned at tag 1.23) and is not redistributed in this
source tree; its own LICENSE applies.