Security Policy¶

Reporting a Vulnerability¶

Send a private email to the maintainer if vulnerabilities were found.

Known Bugs in `art_modern`¶

See News.md for details of the bugs fixed in each release.

Known Build-Time Incompatibilities¶

Clang earlier than 9 with Boost later than 1.78 may raise bugs when using headers from boost/math, since Boost may misidentify Clang as an older GCC that does not support C++11. See here for more details.
Boost versions earlier than 1.65 do not contain boost/asio/thread_pool.hpp or boost/asio/post.hpp. See here for its first introduction. Under these circumstances, try -DUSE_THREAD_PARALLEL=BS in CMake options (introduced below) as an alternative.
GCC 13.3.0 on Haiku OS hrev58590 may cause a kernel panic that locks up the entire system during builds.
GCC would fail on Debian GNU/Hurd.
External HTSLib and NCBI NGS library incompatibilities: Both library defines string_dup.
Builds that use Intel MKL or Intel C++/DPC++ compilers may be incompatible with Citrix Workspace app 25.08.10.111 under Linux.

Known Bugs in Original ART¶

Original ART may Produce Illegal SAM Files¶

Original ART Profile Builder Problem¶

The original ART profile builder would generate profiles with quality scores offset by 1.

Steps to reproduce:

Given file noqual_test/1.1.fq where qualities are all ! (Phred-score 0):

@1/1
AGCTAGCTAGCTAGCTAGCT
+
!!!!!!!!!!!!!!!!!!!!

and file noqual_test/1.2.fq:

@1/2
AGCTAGCTAGCTAGCTAGCT
+
!!!!!!!!!!!!!!!!!!!!

and file opt/noqual_test/ref.fa:

>a
AGCTAGCTACAGCTAGCTACAGCTAGCTACAGCTAGCTACAGCTAGCTACAGCTAGCTACTGATCG

Create a profile with the command:

art_profiler_illumina opt/noqual_test/noqual_test_ opt/noqual_test fq

And then use the original ART to generate reads with the created profile:

art_illumina \
    --in opt/noqual_test/ref.fa \
    --out opt/noqual_test/art_out \
    --qprof1 opt/noqual_test/noqual_test_R1.txt \
    --rcount 2 --len 20 -amp --samout --maskN 0 --rndSeed 0

The generated file will look like:

@a-2
TGCGTATTCGGCCTTTGTTT
+
""""""""""""""""""""
@a-1
CGTAATTATACGCGCATGAG
+
""""""""""""""""""""

The qualities of the generated file will be " (Phred-score 1), instead of ! (Phred-score 0) in the files that generate the profile.